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pipeline.Rmd
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---
title: "Comparsion different program by aligning Arabidopsis genome"
author: "Baoxing Song"
date: "`r format(Sys.Date(), '%Y-%m-%d')`"
output:
html_document:
df_print: paged
word_document: default
pdf_document: default
editor_options:
chunk_output_type: inline
---
Prepare the TAIR10 reference genome sequence in fasta format and genome annotation in gff format
```
wget https://www.arabidopsis.org/download_files/Genes/TAIR10_genome_release/TAIR10_gff3/TAIR10_GFF3_genes.gff
wget ftp://ftp.arabidopsis.org/home/tair/Sequences/whole_chromosomes/TAIR10_chr1.fas
wget ftp://ftp.arabidopsis.org/home/tair/Sequences/whole_chromosomes/TAIR10_chr2.fas
wget ftp://ftp.arabidopsis.org/home/tair/Sequences/whole_chromosomes/TAIR10_chr3.fas
wget ftp://ftp.arabidopsis.org/home/tair/Sequences/whole_chromosomes/TAIR10_chr4.fas
wget ftp://ftp.arabidopsis.org/home/tair/Sequences/whole_chromosomes/TAIR10_chr5.fas
cat TAIR10_chr1.fas TAIR10_chr2.fas TAIR10_chr3.fas TAIR10_chr4.fas TAIR10_chr5.fas > tair10.fa
```
Download the sdi files for 18 Arabidopsis inbreeding lines
```
wget http://mtweb.cs.ucl.ac.uk/mus/www/19genomes/variants.SDI/bur_0.v7c.sdi
wget http://mtweb.cs.ucl.ac.uk/mus/www/19genomes/variants.SDI/can_0.v7c.sdi
wget http://mtweb.cs.ucl.ac.uk/mus/www/19genomes/variants.SDI/ct_1.v7c.sdi
wget http://mtweb.cs.ucl.ac.uk/mus/www/19genomes/variants.SDI/edi_0.v7c.sdi
wget http://mtweb.cs.ucl.ac.uk/mus/www/19genomes/variants.SDI/hi_0.v7c.sdi
wget http://mtweb.cs.ucl.ac.uk/mus/www/19genomes/variants.SDI/kn_0.v7c.sdi
wget http://mtweb.cs.ucl.ac.uk/mus/www/19genomes/variants.SDI/ler_0.v7c.sdi
wget http://mtweb.cs.ucl.ac.uk/mus/www/19genomes/variants.SDI/mt_0.v7c.sdi
wget http://mtweb.cs.ucl.ac.uk/mus/www/19genomes/variants.SDI/no_0.v7c.sdi
wget http://mtweb.cs.ucl.ac.uk/mus/www/19genomes/variants.SDI/oy_0.v7c.sdi
wget http://mtweb.cs.ucl.ac.uk/mus/www/19genomes/variants.SDI/po_0.v7c.sdi
wget http://mtweb.cs.ucl.ac.uk/mus/www/19genomes/variants.SDI/rsch_4.v7c.sdi
wget http://mtweb.cs.ucl.ac.uk/mus/www/19genomes/variants.SDI/sf_2.v7c.sdi
wget http://mtweb.cs.ucl.ac.uk/mus/www/19genomes/variants.SDI/tsu_0.v7c.sdi
wget http://mtweb.cs.ucl.ac.uk/mus/www/19genomes/variants.SDI/wil_2.v7c.sdi
wget http://mtweb.cs.ucl.ac.uk/mus/www/19genomes/variants.SDI/ws_0.v7c.sdi
wget http://mtweb.cs.ucl.ac.uk/mus/www/19genomes/variants.SDI/wu_0.v7c.sdi
wget http://mtweb.cs.ucl.ac.uk/mus/www/19genomes/variants.SDI/zu_0.v7c.sdi
```
Generate synthesis genome sequences using the software GEAN https://github.com/baoxingsong/GEAN/ \
PLEASE NOTE: GEAN gave error message with the downloaded SDI file for ler_0 no_0 and oy_0.
We removed the records
```
Chr4 6020491 12 AAGACATCAATATCATCAGGAAAAATACTCATTCTATTATTAG TAATGACTTAGAGAATAAACTACGAATACAAAAAAAAAAACTCATTATATATCAT 5
Chr4 6020491 33 - TAATGACTTAGAGAATAAACTACGAATACAAAA 4
```
from ler_0.v7c.sdi,\
And removed
```
Chr5 8499298 -1 CAACAAGTTAAAGATTTAAGGTTTTAAAATCCATTTTATAAATAAATTTTTATTGCAAAACTATATTGGAAATCAGAGAAATTTGAAAAATTCACTTTTAAAGTTTTTTAATAACTGATAACGTACTACTTCAAAAACTGTAAACCAAATGCTAAGAATGCATATATGTTTCTGGCAACAAAGAGATAACAGATA GAGTGATAAAAAGATAAATAGCCTATCTTTTTGTTGGATATCCAACAAGTTGAAGGTTAAGGTTTTAAAAGATCCCAGTTTATAGCAAAACTTAAGTTAGAAATCAGAGATATATATTTACAAAAATCACTATTCAATTTTTTTTATAATTGATTACTACTTCAAAAACTAGAAACCAAAAGCCAAGAATGTAT 5
Chr5 8499298 42 - GAGTGATAAAAAGATAAATAGCCTATCTTTTTGTTGGATATC 4
```
from no_0.v7c.sdi, and removed
```
Chr2 7677637 7 ACAAGATAAATATTTAAAAATATATTTCTTAGA GCTAAAGTAATGAAAAAGTGTTTCTAAAACACTAGTTAAT 5
Chr2 7677637 8 - GCTAAAGT 4
```
from oy_0.v7c.sdi manually.
```
gean pseudogeno -r tair10.fa -v bur_0.v7c.sdi -o bur_0.fa
gean pseudogeno -r tair10.fa -v can_0.v7c.sdi -o can_0.fa
gean pseudogeno -r tair10.fa -v ct_1.v7c.sdi -o ct_1.fa
gean pseudogeno -r tair10.fa -v edi_0.v7c.sdi -o edi_0.fa
gean pseudogeno -r tair10.fa -v hi_0.v7c.sdi -o hi_0.fa
gean pseudogeno -r tair10.fa -v kn_0.v7c.sdi -o kn_0.fa
gean pseudogeno -r tair10.fa -v ler_0.v7c.sdi -o ler_0.fa
gean pseudogeno -r tair10.fa -v mt_0.v7c.sdi -o mt_0.fa
gean pseudogeno -r tair10.fa -v no_0.v7c.sdi -o no_0.fa
gean pseudogeno -r tair10.fa -v oy_0.v7c.sdi -o oy_0.fa
gean pseudogeno -r tair10.fa -v po_0.v7c.sdi -o po_0.fa
gean pseudogeno -r tair10.fa -v rsch_4.v7c.sdi -o rsch_4.fa
gean pseudogeno -r tair10.fa -v sf_2.v7c.sdi -o sf_2.fa
gean pseudogeno -r tair10.fa -v tsu_0.v7c.sdi -o tsu_0.fa
gean pseudogeno -r tair10.fa -v wil_2.v7c.sdi -o wil_2.fa
gean pseudogeno -r tair10.fa -v ws_0.v7c.sdi -o ws_0.fa
gean pseudogeno -r tair10.fa -v wu_0.v7c.sdi -o wu_0.fa
gean pseudogeno -r tair10.fa -v zu_0.v7c.sdi -o zu_0.fa
```
Check the variants length distribution
```
awk '{ print length($4)"\t"length($5) }' bur_0.v7c.sdi > bur_0.v7c.sdi.length
awk '{ print length($4)"\t"length($5) }' can_0.v7c.sdi > can_0.v7c.sdi.length
awk '{ print length($4)"\t"length($5) }' ct_1.v7c.sdi > ct_1.v7c.sdi.length
awk '{ print length($4)"\t"length($5) }' edi_0.v7c.sdi > edi_0.v7c.sdi.length
awk '{ print length($4)"\t"length($5) }' hi_0.v7c.sdi > hi_0.v7c.sdi.length
awk '{ print length($4)"\t"length($5) }' kn_0.v7c.sdi > kn_0.v7c.sdi.length
awk '{ print length($4)"\t"length($5) }' ler_0.v7c.sdi > ler_0.v7c.sdi.length
awk '{ print length($4)"\t"length($5) }' mt_0.v7c.sdi > mt_0.v7c.sdi.length
awk '{ print length($4)"\t"length($5) }' no_0.v7c.sdi > no_0.v7c.sdi.length
awk '{ print length($4)"\t"length($5) }' oy_0.v7c.sdi > oy_0.v7c.sdi.length
awk '{ print length($4)"\t"length($5) }' po_0.v7c.sdi > po_0.v7c.sdi.length
awk '{ print length($4)"\t"length($5) }' rsch_4.v7c.sdi > rsch_4.v7c.sdi.length
awk '{ print length($4)"\t"length($5) }' sf_2.v7c.sdi > sf_2.v7c.sdi.length
awk '{ print length($4)"\t"length($5) }' tsu_0.v7c.sdi > tsu_0.v7c.sdi.length
awk '{ print length($4)"\t"length($5) }' wil_2.v7c.sdi > wil_2.v7c.sdi.length
awk '{ print length($4)"\t"length($5) }' ws_0.v7c.sdi > ws_0.v7c.sdi.length
awk '{ print length($4)"\t"length($5) }' wu_0.v7c.sdi > wu_0.v7c.sdi.length
awk '{ print length($4)"\t"length($5) }' zu_0.v7c.sdi > zu_0.v7c.sdi.length
samtools faidx tair10.fa
```
Plot variants length distribution
```{r warning=FALSE}
faidx = read.table("tair10.fa.fai")
genome_size = sum(faidx$V2)
library(ggplot2)
library(data.table)
library(dplyr)
variant_length_distribution <- function(accession) {
dat = read.table(accession)
print ( paste("Total number of variant sites affected reference genome:", sum(dat$V1), sep="") )
print ( paste("Total number of variant sites with length >= 50bp affected reference genome:", sum(dat[which(dat$V1>=50),]$V1), sep="") )
print ( paste("Total number of variants affected reference genome:", sum(dat$V1)/genome_size, sep="") )
print ( paste("Total length of variants with length >= 50bp affected reference genome:", sum(dat[which(dat$V1>=50),]$V1)/genome_size, sep="") )
dat$length = dat$V1
dat[which(dat$V1 < dat$V2),]$length = dat[which(dat$V1 < dat$V2),]$V2
df<- dat[order(dat$length),] %>% mutate(CUMFREQ=cumsum(length))
p = ggplot(data=df, aes(x=length, y=CUMFREQ)) + geom_area( fill = "#00BFC4", position = 'identity') + labs(x="Variant length", y="Cumulative length", fill="", title="") + xlim(0, 65000) + ylim(0, 5200000)+
theme_grey(base_size = 36) +
theme(axis.line = element_blank(), panel.background = element_blank(),panel.border = element_rect(fill=NA,color="black", size=0.5, linetype="solid") )
print(p)
}
variant_length_distribution("bur_0.v7c.sdi.length")
variant_length_distribution("can_0.v7c.sdi.length")
variant_length_distribution("ct_1.v7c.sdi.length")
variant_length_distribution("edi_0.v7c.sdi.length")
variant_length_distribution("hi_0.v7c.sdi.length")
variant_length_distribution("kn_0.v7c.sdi.length")
variant_length_distribution("ler_0.v7c.sdi.length")
variant_length_distribution("mt_0.v7c.sdi.length")
variant_length_distribution("no_0.v7c.sdi.length")
variant_length_distribution("oy_0.v7c.sdi.length")
variant_length_distribution("po_0.v7c.sdi.length")
variant_length_distribution("rsch_4.v7c.sdi.length")
variant_length_distribution("sf_2.v7c.sdi.length")
variant_length_distribution("tsu_0.v7c.sdi.length")
variant_length_distribution("wil_2.v7c.sdi.length")
variant_length_distribution("ws_0.v7c.sdi.length")
variant_length_distribution("wu_0.v7c.sdi.length")
variant_length_distribution("zu_0.v7c.sdi.length")
```
Transform sdi file into maf format
```
anchorwave sdiToMaf -o col_bur.maf -r tair10.fa -s bur_0.v7c.sdi -q bur_0.fa
anchorwave sdiToMaf -o col_can.maf -r tair10.fa -s can_0.v7c.sdi -q can_0.fa
anchorwave sdiToMaf -o col_ct.maf -r tair10.fa -s ct_1.v7c.sdi -q ct_1.fa
anchorwave sdiToMaf -o col_edi.maf -r tair10.fa -s edi_0.v7c.sdi -q edi_0.fa
anchorwave sdiToMaf -o col_hi.maf -r tair10.fa -s hi_0.v7c.sdi -q hi_0.fa
anchorwave sdiToMaf -o col_kn.maf -r tair10.fa -s kn_0.v7c.sdi -q kn_0.fa
anchorwave sdiToMaf -o col_ler.maf -r tair10.fa -s ler_0.v7c.sdi -q ler_0.fa
anchorwave sdiToMaf -o col_mt.maf -r tair10.fa -s mt_0.v7c.sdi -q mt_0.fa
anchorwave sdiToMaf -o col_no.maf -r tair10.fa -s no_0.v7c.sdi -q no_0.fa
anchorwave sdiToMaf -o col_oy.maf -r tair10.fa -s oy_0.v7c.sdi -q oy_0.fa
anchorwave sdiToMaf -o col_po.maf -r tair10.fa -s po_0.v7c.sdi -q po_0.fa
anchorwave sdiToMaf -o col_rsch.maf -r tair10.fa -s rsch_4.v7c.sdi -q rsch_4.fa
anchorwave sdiToMaf -o col_sf.maf -r tair10.fa -s sf_2.v7c.sdi -q sf_2.fa
anchorwave sdiToMaf -o col_tsu.maf -r tair10.fa -s tsu_0.v7c.sdi -q tsu_0.fa
anchorwave sdiToMaf -o col_wil.maf -r tair10.fa -s wil_2.v7c.sdi -q wil_2.fa
anchorwave sdiToMaf -o col_ws.maf -r tair10.fa -s ws_0.v7c.sdi -q ws_0.fa
anchorwave sdiToMaf -o col_wu.maf -r tair10.fa -s wu_0.v7c.sdi -q wu_0.fa
anchorwave sdiToMaf -o col_zu.maf -r tair10.fa -s zu_0.v7c.sdi -q zu_0.fa
```
Using AnchorWave to extract full-length CDS. \
NOTE: please do NOT use CDS extracted using other software and do NOT use the output full-length CDS file for other purpose. Since AnchorWave filtered some CDS records to minimum the impact of minimap2 limitation on genome alignment that "Minimap2 often misses small exons" (https://github.com/lh3/minimap2#limitations)
```
anchorwave gff2seq -r tair10.fa -i TAIR10_GFF3_genes.gff -o cds.fa
```
Use minimap2 (https://github.com/lh3/minimap2) to map the extracted sequence to the TAIR10 reference genome sequence and synthesis genomes
```
minimap2 -x splice -t 6 -k 12 -a -p 0.4 -N 20 tair10.fa cds.fa > ref.sam
minimap2 -x splice -t 6 -k 12 -a -p 0.4 -N 20 bur_0.fa cds.fa > bur_0.sam
minimap2 -x splice -t 6 -k 12 -a -p 0.4 -N 20 can_0.fa cds.fa > can_0.sam
minimap2 -x splice -t 6 -k 12 -a -p 0.4 -N 20 ct_1.fa cds.fa > ct_1.sam
minimap2 -x splice -t 6 -k 12 -a -p 0.4 -N 20 edi_0.fa cds.fa > edi_0.sam
minimap2 -x splice -t 6 -k 12 -a -p 0.4 -N 20 hi_0.fa cds.fa > hi_0.sam
minimap2 -x splice -t 6 -k 12 -a -p 0.4 -N 20 kn_0.fa cds.fa > kn_0.sam
minimap2 -x splice -t 6 -k 12 -a -p 0.4 -N 20 ler_0.fa cds.fa > ler_0.sam
minimap2 -x splice -t 6 -k 12 -a -p 0.4 -N 20 mt_0.fa cds.fa > mt_0.sam
minimap2 -x splice -t 6 -k 12 -a -p 0.4 -N 20 no_0.fa cds.fa > no_0.sam
minimap2 -x splice -t 6 -k 12 -a -p 0.4 -N 20 oy_0.fa cds.fa > oy_0.sam
minimap2 -x splice -t 6 -k 12 -a -p 0.4 -N 20 po_0.fa cds.fa > po_0.sam
minimap2 -x splice -t 6 -k 12 -a -p 0.4 -N 20 rsch_4.fa cds.fa > rsch_4.sam
minimap2 -x splice -t 6 -k 12 -a -p 0.4 -N 20 sf_2.fa cds.fa > sf_2.sam
minimap2 -x splice -t 6 -k 12 -a -p 0.4 -N 20 tsu_0.fa cds.fa > tsu_0.sam
minimap2 -x splice -t 6 -k 12 -a -p 0.4 -N 20 wil_2.fa cds.fa > wil_2.sam
minimap2 -x splice -t 6 -k 12 -a -p 0.4 -N 20 ws_0.fa cds.fa > ws_0.sam
minimap2 -x splice -t 6 -k 12 -a -p 0.4 -N 20 wu_0.fa cds.fa > wu_0.sam
minimap2 -x splice -t 6 -k 12 -a -p 0.4 -N 20 zu_0.fa cds.fa > zu_0.sam
```
Perform genome alignment using AnchorWave
```
/usr/bin/time anchorwave genoAli -i TAIR10_GFF3_genes.gff -as cds.fa -r tair10.fa -a bur_0.sam -ar ref.sam -s bur_0.fa -v bur_0.vcf -n bur_0.anchors -o bur_0.maf -f bur_0.f.maf -w 38000 -fa3 200000 -B -6 -O1 -8 -E1 -2 -O2 -75 -E2 -1 -t 1 >bur_0.log 2>&1 &
/usr/bin/time anchorwave genoAli -i TAIR10_GFF3_genes.gff -as cds.fa -r tair10.fa -a can_0.sam -ar ref.sam -s can_0.fa -v can_0.vcf -n can_0.anchors -o can_0.maf -f can_0.f.maf -w 38000 -fa3 200000 -B -6 -O1 -8 -E1 -2 -O2 -75 -E2 -1 -t 1 >can_0.log 2>&1 &
/usr/bin/time anchorwave genoAli -i TAIR10_GFF3_genes.gff -as cds.fa -r tair10.fa -a ct_1.sam -ar ref.sam -s ct_1.fa -v ct_1.vcf -n ct_1.anchors -o ct_1.maf -f ct_1.f.maf -w 38000 -fa3 200000 -B -6 -O1 -8 -E1 -2 -O2 -75 -E2 -1 -t 1 >ct_1.log 2>&1 &
/usr/bin/time anchorwave genoAli -i TAIR10_GFF3_genes.gff -as cds.fa -r tair10.fa -a edi_0.sam -ar ref.sam -s edi_0.fa -v edi_0.vcf -n edi_0.anchors -o edi_0.maf -f edi_0.f.maf -w 38000 -fa3 200000 -B -6 -O1 -8 -E1 -2 -O2 -75 -E2 -1 -t 1 >edi_0.log 2>&1 &
/usr/bin/time anchorwave genoAli -i TAIR10_GFF3_genes.gff -as cds.fa -r tair10.fa -a hi_0.sam -ar ref.sam -s hi_0.fa -v hi_0.vcf -n hi_0.anchors -o hi_0.maf -f hi_0.f.maf -w 38000 -fa3 200000 -B -6 -O1 -8 -E1 -2 -O2 -75 -E2 -1 -t 1 >hi_0.log 2>&1 &
/usr/bin/time anchorwave genoAli -i TAIR10_GFF3_genes.gff -as cds.fa -r tair10.fa -a kn_0.sam -ar ref.sam -s kn_0.fa -v kn_0.vcf -n kn_0.anchors -o kn_0.maf -f kn_0.f.maf -w 38000 -fa3 200000 -B -6 -O1 -8 -E1 -2 -O2 -75 -E2 -1 -t 1 >kn_0.log 2>&1 &
/usr/bin/time anchorwave genoAli -i TAIR10_GFF3_genes.gff -as cds.fa -r tair10.fa -a ler_0.sam -ar ref.sam -s ler_0.fa -v ler_0.vcf -n ler_0.anchors -o ler_0.maf -f ler_0.f.maf -w 38000 -fa3 200000 -B -6 -O1 -8 -E1 -2 -O2 -75 -E2 -1 -t 1 >ler_0.log 2>&1 &
/usr/bin/time anchorwave genoAli -i TAIR10_GFF3_genes.gff -as cds.fa -r tair10.fa -a mt_0.sam -ar ref.sam -s mt_0.fa -v mt_0.vcf -n mt_0.anchors -o mt_0.maf -f mt_0.f.maf -w 38000 -fa3 200000 -B -6 -O1 -8 -E1 -2 -O2 -75 -E2 -1 -t 1 >mt_0.log 2>&1 &
/usr/bin/time anchorwave genoAli -i TAIR10_GFF3_genes.gff -as cds.fa -r tair10.fa -a no_0.sam -ar ref.sam -s no_0.fa -v no_0.vcf -n no_0.anchors -o no_0.maf -f no_0.f.maf -w 38000 -fa3 200000 -B -6 -O1 -8 -E1 -2 -O2 -75 -E2 -1 -t 1 >no_0.log 2>&1 &
/usr/bin/time anchorwave genoAli -i TAIR10_GFF3_genes.gff -as cds.fa -r tair10.fa -a oy_0.sam -ar ref.sam -s oy_0.fa -v oy_0.vcf -n oy_0.anchors -o oy_0.maf -f oy_0.f.maf -w 38000 -fa3 200000 -B -6 -O1 -8 -E1 -2 -O2 -75 -E2 -1 -t 1 >oy_0.log 2>&1 &
/usr/bin/time anchorwave genoAli -i TAIR10_GFF3_genes.gff -as cds.fa -r tair10.fa -a po_0.sam -ar ref.sam -s po_0.fa -v po_0.vcf -n po_0.anchors -o po_0.maf -f po_0.f.maf -w 38000 -fa3 200000 -B -6 -O1 -8 -E1 -2 -O2 -75 -E2 -1 -t 1 >po_0.log 2>&1 &
/usr/bin/time anchorwave genoAli -i TAIR10_GFF3_genes.gff -as cds.fa -r tair10.fa -a rsch_4.sam -ar ref.sam -s rsch_4.fa -v rsch_4.vcf -n rsch_4.anchors -o rsch_4.maf -f rsch_4.f.maf -w 38000 -fa3 200000 -B -6 -O1 -8 -E1 -2 -O2 -75 -E2 -1 -t 1 >rsch_4.log 2>&1 &
/usr/bin/time anchorwave genoAli -i TAIR10_GFF3_genes.gff -as cds.fa -r tair10.fa -a sf_2.sam -ar ref.sam -s sf_2.fa -v sf_2.vcf -n sf_2.anchors -o sf_2.maf -f sf_2.f.maf -w 38000 -fa3 200000 -B -6 -O1 -8 -E1 -2 -O2 -75 -E2 -1 -t 1 >sf_2.log 2>&1 &
/usr/bin/time anchorwave genoAli -i TAIR10_GFF3_genes.gff -as cds.fa -r tair10.fa -a tsu_0.sam -ar ref.sam -s tsu_0.fa -v tsu_0.vcf -n tsu_0.anchors -o tsu_0.maf -f tsu_0.f.maf -w 38000 -fa3 200000 -B -6 -O1 -8 -E1 -2 -O2 -75 -E2 -1 -t 1 >tsu_0.log 2>&1 &
/usr/bin/time anchorwave genoAli -i TAIR10_GFF3_genes.gff -as cds.fa -r tair10.fa -a wil_2.sam -ar ref.sam -s wil_2.fa -v wil_2.vcf -n wil_2.anchors -o wil_2.maf -f wil_2.f.maf -w 38000 -fa3 200000 -B -6 -O1 -8 -E1 -2 -O2 -75 -E2 -1 -t 1 >wil_2.log 2>&1 &
/usr/bin/time anchorwave genoAli -i TAIR10_GFF3_genes.gff -as cds.fa -r tair10.fa -a ws_0.sam -ar ref.sam -s ws_0.fa -v ws_0.vcf -n ws_0.anchors -o ws_0.maf -f ws_0.f.maf -w 38000 -fa3 200000 -B -6 -O1 -8 -E1 -2 -O2 -75 -E2 -1 -t 1 >ws_0.log 2>&1 &
/usr/bin/time anchorwave genoAli -i TAIR10_GFF3_genes.gff -as cds.fa -r tair10.fa -a wu_0.sam -ar ref.sam -s wu_0.fa -v wu_0.vcf -n wu_0.anchors -o wu_0.maf -f wu_0.f.maf -w 38000 -fa3 200000 -B -6 -O1 -8 -E1 -2 -O2 -75 -E2 -1 -t 1 >wu_0.log 2>&1 &
/usr/bin/time anchorwave genoAli -i TAIR10_GFF3_genes.gff -as cds.fa -r tair10.fa -a zu_0.sam -ar ref.sam -s zu_0.fa -v zu_0.vcf -n zu_0.anchors -o zu_0.maf -f zu_0.f.maf -w 38000 -fa3 200000 -B -6 -O1 -8 -E1 -2 -O2 -75 -E2 -1 -t 1 >zu_0.log 2>&1 &
```
Compare produced genome alignment with benchmark genome alignment \
CompareMafAndCheckMafCoverage.py is a script included in the released code and located at ./src/tests/scripts/CompareMafAndCheckMafCoverage.py
```
sed -i 's/tair10.fa./col./g' bur_0.maf
sed -i 's/bur_0.fa./query./g' bur_0.maf
sed -i 's/tair10.fa./col./g' can_0.maf
sed -i 's/can_0.fa./query./g' can_0.maf
sed -i 's/tair10.fa./col./g' ct_1.maf
sed -i 's/ct_1.fa./query./g' ct_1.maf
sed -i 's/tair10.fa./col./g' edi_0.maf
sed -i 's/edi_0.fa./query./g' edi_0.maf
sed -i 's/tair10.fa./col./g' hi_0.maf
sed -i 's/hi_0.fa./query./g' hi_0.maf
sed -i 's/tair10.fa./col./g' kn_0.maf
sed -i 's/kn_0.fa./query./g' kn_0.maf
sed -i 's/tair10.fa./col./g' ler_0.maf
sed -i 's/ler_0.fa./query./g' ler_0.maf
sed -i 's/tair10.fa./col./g' mt_0.maf
sed -i 's/mt_0.fa./query./g' mt_0.maf
sed -i 's/tair10.fa./col./g' no_0.maf
sed -i 's/no_0.fa./query./g' no_0.maf
sed -i 's/tair10.fa./col./g' oy_0.maf
sed -i 's/oy_0.fa./query./g' oy_0.maf
sed -i 's/tair10.fa./col./g' po_0.maf
sed -i 's/po_0.fa./query./g' po_0.maf
sed -i 's/tair10.fa./col./g' rsch_4.maf
sed -i 's/rsch_4.fa./query./g' rsch_4.maf
sed -i 's/tair10.fa./col./g' sf_2.maf
sed -i 's/sf_2.fa./query./g' sf_2.maf
sed -i 's/tair10.fa./col./g' tsu_0.maf
sed -i 's/tsu_0.fa./query./g' tsu_0.maf
sed -i 's/tair10.fa./col./g' wil_2.maf
sed -i 's/wil_2.fa./query./g' wil_2.maf
sed -i 's/tair10.fa./col./g' ws_0.maf
sed -i 's/ws_0.fa./query./g' ws_0.maf
sed -i 's/tair10.fa./col./g' wu_0.maf
sed -i 's/wu_0.fa./query./g' wu_0.maf
sed -i 's/tair10.fa./col./g' zu_0.maf
sed -i 's/zu_0.fa./query./g' zu_0.maf
python3 CompareMafAndCheckMafCoverage.py ./col_bur.maf bur_0.maf &
python3 CompareMafAndCheckMafCoverage.py ./col_can.maf can_0.maf &
python3 CompareMafAndCheckMafCoverage.py ./col_ct.maf ct_1.maf &
python3 CompareMafAndCheckMafCoverage.py ./col_edi.maf edi_0.maf &
python3 CompareMafAndCheckMafCoverage.py ./col_hi.maf hi_0.maf &
python3 CompareMafAndCheckMafCoverage.py ./col_kn.maf kn_0.maf &
python3 CompareMafAndCheckMafCoverage.py ./col_ler.maf ler_0.maf &
python3 CompareMafAndCheckMafCoverage.py ./col_mt.maf mt_0.maf &
python3 CompareMafAndCheckMafCoverage.py ./col_no.maf no_0.maf &
python3 CompareMafAndCheckMafCoverage.py ./col_oy.maf oy_0.maf &
python3 CompareMafAndCheckMafCoverage.py ./col_po.maf po_0.maf &
python3 CompareMafAndCheckMafCoverage.py ./col_rsch.maf rsch_4.maf &
python3 CompareMafAndCheckMafCoverage.py ./col_sf.maf sf_2.maf &
python3 CompareMafAndCheckMafCoverage.py ./col_tsu.maf tsu_0.maf &
python3 CompareMafAndCheckMafCoverage.py ./col_wil.maf wil_2.maf &
python3 CompareMafAndCheckMafCoverage.py ./col_ws.maf ws_0.maf &
python3 CompareMafAndCheckMafCoverage.py ./col_wu.maf wu_0.maf &
python3 CompareMafAndCheckMafCoverage.py ./col_zu.maf zu_0.maf &
python3 CompareMafAndCheckMafCoverageAll.py ./col_bur.maf bur_0.maf &
python3 CompareMafAndCheckMafCoverageAll.py ./col_can.maf can_0.maf &
python3 CompareMafAndCheckMafCoverageAll.py ./col_ct.maf ct_1.maf &
python3 CompareMafAndCheckMafCoverageAll.py ./col_edi.maf edi_0.maf &
python3 CompareMafAndCheckMafCoverageAll.py ./col_hi.maf hi_0.maf &
python3 CompareMafAndCheckMafCoverageAll.py ./col_kn.maf kn_0.maf &
python3 CompareMafAndCheckMafCoverageAll.py ./col_ler.maf ler_0.maf &
python3 CompareMafAndCheckMafCoverageAll.py ./col_mt.maf mt_0.maf &
python3 CompareMafAndCheckMafCoverageAll.py ./col_no.maf no_0.maf &
python3 CompareMafAndCheckMafCoverageAll.py ./col_oy.maf oy_0.maf &
python3 CompareMafAndCheckMafCoverageAll.py ./col_po.maf po_0.maf &
python3 CompareMafAndCheckMafCoverageAll.py ./col_rsch.maf rsch_4.maf &
python3 CompareMafAndCheckMafCoverageAll.py ./col_sf.maf sf_2.maf &
python3 CompareMafAndCheckMafCoverageAll.py ./col_tsu.maf tsu_0.maf &
python3 CompareMafAndCheckMafCoverageAll.py ./col_wil.maf wil_2.maf &
python3 CompareMafAndCheckMafCoverageAll.py ./col_ws.maf ws_0.maf &
python3 CompareMafAndCheckMafCoverageAll.py ./col_wu.maf wu_0.maf &
python3 CompareMafAndCheckMafCoverageAll.py ./col_zu.maf zu_0.maf &
```
Perform genome alignment using minimap2
```
/usr/bin/time minimap2 -x asm5 -t 1 -a tair10.fa bur_0.fa > minimap2_asm5_bur_0.sam 2> minimap2_asm5_bur_0.log &
/usr/bin/time minimap2 -x asm5 -t 1 -a tair10.fa can_0.fa > minimap2_asm5_can_0.sam 2> minimap2_asm5_can_0.log &
/usr/bin/time minimap2 -x asm5 -t 1 -a tair10.fa ct_1.fa > minimap2_asm5_ct_1.sam 2> minimap2_asm5_ct_1.log &
/usr/bin/time minimap2 -x asm5 -t 1 -a tair10.fa edi_0.fa > minimap2_asm5_edi_0.sam 2> minimap2_asm5_edi_0.log &
/usr/bin/time minimap2 -x asm5 -t 1 -a tair10.fa hi_0.fa > minimap2_asm5_hi_0.sam 2> minimap2_asm5_hi_0.log &
/usr/bin/time minimap2 -x asm5 -t 1 -a tair10.fa kn_0.fa > minimap2_asm5_kn_0.sam 2> minimap2_asm5_kn_0.log &
/usr/bin/time minimap2 -x asm5 -t 1 -a tair10.fa ler_0.fa > minimap2_asm5_ler_0.sam 2> minimap2_asm5_ler_0.log &
/usr/bin/time minimap2 -x asm5 -t 1 -a tair10.fa mt_0.fa > minimap2_asm5_mt_0.sam 2> minimap2_asm5_mt_0.log &
/usr/bin/time minimap2 -x asm5 -t 1 -a tair10.fa no_0.fa > minimap2_asm5_no_0.sam 2> minimap2_asm5_no_0.log &
/usr/bin/time minimap2 -x asm5 -t 1 -a tair10.fa oy_0.fa > minimap2_asm5_oy_0.sam 2> minimap2_asm5_oy_0.log &
/usr/bin/time minimap2 -x asm5 -t 1 -a tair10.fa po_0.fa > minimap2_asm5_po_0.sam 2> minimap2_asm5_po_0.log &
/usr/bin/time minimap2 -x asm5 -t 1 -a tair10.fa rsch_4.fa > minimap2_asm5_rsch_4.sam 2> minimap2_asm5_rsch_4.log &
/usr/bin/time minimap2 -x asm5 -t 1 -a tair10.fa sf_2.fa > minimap2_asm5_sf_2.sam 2> minimap2_asm5_sf_2.log &
/usr/bin/time minimap2 -x asm5 -t 1 -a tair10.fa tsu_0.fa > minimap2_asm5_tsu_0.sam 2> minimap2_asm5_tsu_0.log &
/usr/bin/time minimap2 -x asm5 -t 1 -a tair10.fa wil_2.fa > minimap2_asm5_wil_2.sam 2> minimap2_asm5_wil_2.log &
/usr/bin/time minimap2 -x asm5 -t 1 -a tair10.fa ws_0.fa > minimap2_asm5_ws_0.sam 2> minimap2_asm5_ws_0.log &
/usr/bin/time minimap2 -x asm5 -t 1 -a tair10.fa wu_0.fa > minimap2_asm5_wu_0.sam 2> minimap2_asm5_wu_0.log &
/usr/bin/time minimap2 -x asm5 -t 1 -a tair10.fa zu_0.fa > minimap2_asm5_zu_0.sam 2> minimap2_asm5_zu_0.log &
/usr/bin/time minimap2 -x asm10 -t 1 -a tair10.fa bur_0.fa > minimap2_asm10_bur_0.sam 2> minimap2_asm10_bur_0.log &
/usr/bin/time minimap2 -x asm10 -t 1 -a tair10.fa can_0.fa > minimap2_asm10_can_0.sam 2> minimap2_asm10_can_0.log &
/usr/bin/time minimap2 -x asm10 -t 1 -a tair10.fa ct_1.fa > minimap2_asm10_ct_1.sam 2> minimap2_asm10_ct_1.log &
/usr/bin/time minimap2 -x asm10 -t 1 -a tair10.fa edi_0.fa > minimap2_asm10_edi_0.sam 2> minimap2_asm10_edi_0.log &
/usr/bin/time minimap2 -x asm10 -t 1 -a tair10.fa hi_0.fa > minimap2_asm10_hi_0.sam 2> minimap2_asm10_hi_0.log &
/usr/bin/time minimap2 -x asm10 -t 1 -a tair10.fa kn_0.fa > minimap2_asm10_kn_0.sam 2> minimap2_asm10_kn_0.log &
/usr/bin/time minimap2 -x asm10 -t 1 -a tair10.fa ler_0.fa > minimap2_asm10_ler_0.sam 2> minimap2_asm10_ler_0.log &
/usr/bin/time minimap2 -x asm10 -t 1 -a tair10.fa mt_0.fa > minimap2_asm10_mt_0.sam 2> minimap2_asm10_mt_0.log &
/usr/bin/time minimap2 -x asm10 -t 1 -a tair10.fa no_0.fa > minimap2_asm10_no_0.sam 2> minimap2_asm10_no_0.log &
/usr/bin/time minimap2 -x asm10 -t 1 -a tair10.fa oy_0.fa > minimap2_asm10_oy_0.sam 2> minimap2_asm10_oy_0.log &
/usr/bin/time minimap2 -x asm10 -t 1 -a tair10.fa po_0.fa > minimap2_asm10_po_0.sam 2> minimap2_asm10_po_0.log &
/usr/bin/time minimap2 -x asm10 -t 1 -a tair10.fa rsch_4.fa > minimap2_asm10_rsch_4.sam 2> minimap2_asm10_rsch_4.log &
/usr/bin/time minimap2 -x asm10 -t 1 -a tair10.fa sf_2.fa > minimap2_asm10_sf_2.sam 2> minimap2_asm10_sf_2.log &
/usr/bin/time minimap2 -x asm10 -t 1 -a tair10.fa tsu_0.fa > minimap2_asm10_tsu_0.sam 2> minimap2_asm10_tsu_0.log &
/usr/bin/time minimap2 -x asm10 -t 1 -a tair10.fa wil_2.fa > minimap2_asm10_wil_2.sam 2> minimap2_asm10_wil_2.log &
/usr/bin/time minimap2 -x asm10 -t 1 -a tair10.fa ws_0.fa > minimap2_asm10_ws_0.sam 2> minimap2_asm10_ws_0.log &
/usr/bin/time minimap2 -x asm10 -t 1 -a tair10.fa wu_0.fa > minimap2_asm10_wu_0.sam 2> minimap2_asm10_wu_0.log &
/usr/bin/time minimap2 -x asm10 -t 1 -a tair10.fa zu_0.fa > minimap2_asm10_zu_0.sam 2> minimap2_asm10_zu_0.log &
/usr/bin/time minimap2 -x asm20 -t 1 -a tair10.fa bur_0.fa > minimap2_asm20_bur_0.sam 2> minimap2_asm20_bur_0.log &
/usr/bin/time minimap2 -x asm20 -t 1 -a tair10.fa can_0.fa > minimap2_asm20_can_0.sam 2> minimap2_asm20_can_0.log &
/usr/bin/time minimap2 -x asm20 -t 1 -a tair10.fa ct_1.fa > minimap2_asm20_ct_1.sam 2> minimap2_asm20_ct_1.log &
/usr/bin/time minimap2 -x asm20 -t 1 -a tair10.fa edi_0.fa > minimap2_asm20_edi_0.sam 2> minimap2_asm20_edi_0.log &
/usr/bin/time minimap2 -x asm20 -t 1 -a tair10.fa hi_0.fa > minimap2_asm20_hi_0.sam 2> minimap2_asm20_hi_0.log &
/usr/bin/time minimap2 -x asm20 -t 1 -a tair10.fa kn_0.fa > minimap2_asm20_kn_0.sam 2> minimap2_asm20_kn_0.log &
/usr/bin/time minimap2 -x asm20 -t 1 -a tair10.fa ler_0.fa > minimap2_asm20_ler_0.sam 2> minimap2_asm20_ler_0.log &
/usr/bin/time minimap2 -x asm20 -t 1 -a tair10.fa mt_0.fa > minimap2_asm20_mt_0.sam 2> minimap2_asm20_mt_0.log &
/usr/bin/time minimap2 -x asm20 -t 1 -a tair10.fa no_0.fa > minimap2_asm20_no_0.sam 2> minimap2_asm20_no_0.log &
/usr/bin/time minimap2 -x asm20 -t 1 -a tair10.fa oy_0.fa > minimap2_asm20_oy_0.sam 2> minimap2_asm20_oy_0.log &
/usr/bin/time minimap2 -x asm20 -t 1 -a tair10.fa po_0.fa > minimap2_asm20_po_0.sam 2> minimap2_asm20_po_0.log &
/usr/bin/time minimap2 -x asm20 -t 1 -a tair10.fa rsch_4.fa > minimap2_asm20_rsch_4.sam 2> minimap2_asm20_rsch_4.log &
/usr/bin/time minimap2 -x asm20 -t 1 -a tair10.fa sf_2.fa > minimap2_asm20_sf_2.sam 2> minimap2_asm20_sf_2.log &
/usr/bin/time minimap2 -x asm20 -t 1 -a tair10.fa tsu_0.fa > minimap2_asm20_tsu_0.sam 2> minimap2_asm20_tsu_0.log &
/usr/bin/time minimap2 -x asm20 -t 1 -a tair10.fa wil_2.fa > minimap2_asm20_wil_2.sam 2> minimap2_asm20_wil_2.log &
/usr/bin/time minimap2 -x asm20 -t 1 -a tair10.fa ws_0.fa > minimap2_asm20_ws_0.sam 2> minimap2_asm20_ws_0.log &
/usr/bin/time minimap2 -x asm20 -t 1 -a tair10.fa wu_0.fa > minimap2_asm20_wu_0.sam 2> minimap2_asm20_wu_0.log &
/usr/bin/time minimap2 -x asm20 -t 1 -a tair10.fa zu_0.fa > minimap2_asm20_zu_0.sam 2> minimap2_asm20_zu_0.log &
```
Reformat sam files into maf format
```
anchorwave sam2maf -r tair10.fa -q bur_0.fa -s minimap2_asm5_bur_0.sam -o minimap2_asm5_bur_0.maf
anchorwave sam2maf -r tair10.fa -q can_0.fa -s minimap2_asm5_can_0.sam -o minimap2_asm5_can_0.maf
anchorwave sam2maf -r tair10.fa -q ct_1.fa -s minimap2_asm5_ct_1.sam -o minimap2_asm5_ct_1.maf
anchorwave sam2maf -r tair10.fa -q edi_0.fa -s minimap2_asm5_edi_0.sam -o minimap2_asm5_edi_0.maf
anchorwave sam2maf -r tair10.fa -q hi_0.fa -s minimap2_asm5_hi_0.sam -o minimap2_asm5_hi_0.maf
anchorwave sam2maf -r tair10.fa -q kn_0.fa -s minimap2_asm5_kn_0.sam -o minimap2_asm5_kn_0.maf
anchorwave sam2maf -r tair10.fa -q ler_0.fa -s minimap2_asm5_ler_0.sam -o minimap2_asm5_ler_0.maf
anchorwave sam2maf -r tair10.fa -q mt_0.fa -s minimap2_asm5_mt_0.sam -o minimap2_asm5_mt_0.maf
anchorwave sam2maf -r tair10.fa -q no_0.fa -s minimap2_asm5_no_0.sam -o minimap2_asm5_no_0.maf
anchorwave sam2maf -r tair10.fa -q oy_0.fa -s minimap2_asm5_oy_0.sam -o minimap2_asm5_oy_0.maf
anchorwave sam2maf -r tair10.fa -q po_0.fa -s minimap2_asm5_po_0.sam -o minimap2_asm5_po_0.maf
anchorwave sam2maf -r tair10.fa -q rsch_4.fa -s minimap2_asm5_rsch_4.sam -o minimap2_asm5_rsch_4.maf
anchorwave sam2maf -r tair10.fa -q sf_2.fa -s minimap2_asm5_sf_2.sam -o minimap2_asm5_sf_2.maf
anchorwave sam2maf -r tair10.fa -q tsu_0.fa -s minimap2_asm5_tsu_0.sam -o minimap2_asm5_tsu_0.maf
anchorwave sam2maf -r tair10.fa -q wil_2.fa -s minimap2_asm5_wil_2.sam -o minimap2_asm5_wil_2.maf
anchorwave sam2maf -r tair10.fa -q ws_0.fa -s minimap2_asm5_ws_0.sam -o minimap2_asm5_ws_0.maf
anchorwave sam2maf -r tair10.fa -q wu_0.fa -s minimap2_asm5_wu_0.sam -o minimap2_asm5_wu_0.maf
anchorwave sam2maf -r tair10.fa -q zu_0.fa -s minimap2_asm5_zu_0.sam -o minimap2_asm5_zu_0.maf
anchorwave sam2maf -r tair10.fa -q bur_0.fa -s minimap2_asm10_bur_0.sam -o minimap2_asm10_bur_0.maf
anchorwave sam2maf -r tair10.fa -q can_0.fa -s minimap2_asm10_can_0.sam -o minimap2_asm10_can_0.maf
anchorwave sam2maf -r tair10.fa -q ct_1.fa -s minimap2_asm10_ct_1.sam -o minimap2_asm10_ct_1.maf
anchorwave sam2maf -r tair10.fa -q edi_0.fa -s minimap2_asm10_edi_0.sam -o minimap2_asm10_edi_0.maf
anchorwave sam2maf -r tair10.fa -q hi_0.fa -s minimap2_asm10_hi_0.sam -o minimap2_asm10_hi_0.maf
anchorwave sam2maf -r tair10.fa -q kn_0.fa -s minimap2_asm10_kn_0.sam -o minimap2_asm10_kn_0.maf
anchorwave sam2maf -r tair10.fa -q ler_0.fa -s minimap2_asm10_ler_0.sam -o minimap2_asm10_ler_0.maf
anchorwave sam2maf -r tair10.fa -q mt_0.fa -s minimap2_asm10_mt_0.sam -o minimap2_asm10_mt_0.maf
anchorwave sam2maf -r tair10.fa -q no_0.fa -s minimap2_asm10_no_0.sam -o minimap2_asm10_no_0.maf
anchorwave sam2maf -r tair10.fa -q oy_0.fa -s minimap2_asm10_oy_0.sam -o minimap2_asm10_oy_0.maf
anchorwave sam2maf -r tair10.fa -q po_0.fa -s minimap2_asm10_po_0.sam -o minimap2_asm10_po_0.maf
anchorwave sam2maf -r tair10.fa -q rsch_4.fa -s minimap2_asm10_rsch_4.sam -o minimap2_asm10_rsch_4.maf
anchorwave sam2maf -r tair10.fa -q sf_2.fa -s minimap2_asm10_sf_2.sam -o minimap2_asm10_sf_2.maf
anchorwave sam2maf -r tair10.fa -q tsu_0.fa -s minimap2_asm10_tsu_0.sam -o minimap2_asm10_tsu_0.maf
anchorwave sam2maf -r tair10.fa -q wil_2.fa -s minimap2_asm10_wil_2.sam -o minimap2_asm10_wil_2.maf
anchorwave sam2maf -r tair10.fa -q ws_0.fa -s minimap2_asm10_ws_0.sam -o minimap2_asm10_ws_0.maf
anchorwave sam2maf -r tair10.fa -q wu_0.fa -s minimap2_asm10_wu_0.sam -o minimap2_asm10_wu_0.maf
anchorwave sam2maf -r tair10.fa -q zu_0.fa -s minimap2_asm10_zu_0.sam -o minimap2_asm10_zu_0.maf
anchorwave sam2maf -r tair10.fa -q bur_0.fa -s minimap2_asm20_bur_0.sam -o minimap2_asm20_bur_0.maf
anchorwave sam2maf -r tair10.fa -q can_0.fa -s minimap2_asm20_can_0.sam -o minimap2_asm20_can_0.maf
anchorwave sam2maf -r tair10.fa -q ct_1.fa -s minimap2_asm20_ct_1.sam -o minimap2_asm20_ct_1.maf
anchorwave sam2maf -r tair10.fa -q edi_0.fa -s minimap2_asm20_edi_0.sam -o minimap2_asm20_edi_0.maf
anchorwave sam2maf -r tair10.fa -q hi_0.fa -s minimap2_asm20_hi_0.sam -o minimap2_asm20_hi_0.maf
anchorwave sam2maf -r tair10.fa -q kn_0.fa -s minimap2_asm20_kn_0.sam -o minimap2_asm20_kn_0.maf
anchorwave sam2maf -r tair10.fa -q ler_0.fa -s minimap2_asm20_ler_0.sam -o minimap2_asm20_ler_0.maf
anchorwave sam2maf -r tair10.fa -q mt_0.fa -s minimap2_asm20_mt_0.sam -o minimap2_asm20_mt_0.maf
anchorwave sam2maf -r tair10.fa -q no_0.fa -s minimap2_asm20_no_0.sam -o minimap2_asm20_no_0.maf
anchorwave sam2maf -r tair10.fa -q oy_0.fa -s minimap2_asm20_oy_0.sam -o minimap2_asm20_oy_0.maf
anchorwave sam2maf -r tair10.fa -q po_0.fa -s minimap2_asm20_po_0.sam -o minimap2_asm20_po_0.maf
anchorwave sam2maf -r tair10.fa -q rsch_4.fa -s minimap2_asm20_rsch_4.sam -o minimap2_asm20_rsch_4.maf
anchorwave sam2maf -r tair10.fa -q sf_2.fa -s minimap2_asm20_sf_2.sam -o minimap2_asm20_sf_2.maf
anchorwave sam2maf -r tair10.fa -q tsu_0.fa -s minimap2_asm20_tsu_0.sam -o minimap2_asm20_tsu_0.maf
anchorwave sam2maf -r tair10.fa -q wil_2.fa -s minimap2_asm20_wil_2.sam -o minimap2_asm20_wil_2.maf
anchorwave sam2maf -r tair10.fa -q ws_0.fa -s minimap2_asm20_ws_0.sam -o minimap2_asm20_ws_0.maf
anchorwave sam2maf -r tair10.fa -q wu_0.fa -s minimap2_asm20_wu_0.sam -o minimap2_asm20_wu_0.maf
anchorwave sam2maf -r tair10.fa -q zu_0.fa -s minimap2_asm20_zu_0.sam -o minimap2_asm20_zu_0.maf
```
Evaluated the performance of minimap2
```
python3 CompareMafAndCheckMafCoverage.py col_bur.maf minimap2_asm5_bur_0.maf
python3 CompareMafAndCheckMafCoverage.py col_can.maf minimap2_asm5_can_0.maf
python3 CompareMafAndCheckMafCoverage.py col_ct.maf minimap2_asm5_ct_1.maf
python3 CompareMafAndCheckMafCoverage.py col_edi.maf minimap2_asm5_edi_0.maf
python3 CompareMafAndCheckMafCoverage.py col_hi.maf minimap2_asm5_hi_0.maf
python3 CompareMafAndCheckMafCoverage.py col_kn.maf minimap2_asm5_kn_0.maf
python3 CompareMafAndCheckMafCoverage.py col_ler.maf minimap2_asm5_ler_0.maf
python3 CompareMafAndCheckMafCoverage.py col_mt.maf minimap2_asm5_mt_0.maf
python3 CompareMafAndCheckMafCoverage.py col_no.maf minimap2_asm5_no_0.maf
python3 CompareMafAndCheckMafCoverage.py col_oy.maf minimap2_asm5_oy_0.maf
python3 CompareMafAndCheckMafCoverage.py col_po.maf minimap2_asm5_po_0.maf
python3 CompareMafAndCheckMafCoverage.py col_rsch.maf minimap2_asm5_rsch_4.maf
python3 CompareMafAndCheckMafCoverage.py col_sf.maf minimap2_asm5_sf_2.maf
python3 CompareMafAndCheckMafCoverage.py col_tsu.maf minimap2_asm5_tsu_0.maf
python3 CompareMafAndCheckMafCoverage.py col_wil.maf minimap2_asm5_wil_2.maf
python3 CompareMafAndCheckMafCoverage.py col_ws.maf minimap2_asm5_ws_0.maf
python3 CompareMafAndCheckMafCoverage.py col_wu.maf minimap2_asm5_wu_0.maf
python3 CompareMafAndCheckMafCoverage.py col_zu.maf minimap2_asm5_zu_0.maf
python3 CompareMafAndCheckMafCoverage.py col_bur.maf minimap2_asm10_bur_0.maf
python3 CompareMafAndCheckMafCoverage.py col_can.maf minimap2_asm10_can_0.maf
python3 CompareMafAndCheckMafCoverage.py col_ct.maf minimap2_asm10_ct_1.maf
python3 CompareMafAndCheckMafCoverage.py col_edi.maf minimap2_asm10_edi_0.maf
python3 CompareMafAndCheckMafCoverage.py col_hi.maf minimap2_asm10_hi_0.maf
python3 CompareMafAndCheckMafCoverage.py col_kn.maf minimap2_asm10_kn_0.maf
python3 CompareMafAndCheckMafCoverage.py col_ler.maf minimap2_asm10_ler_0.maf
python3 CompareMafAndCheckMafCoverage.py col_mt.maf minimap2_asm10_mt_0.maf
python3 CompareMafAndCheckMafCoverage.py col_no.maf minimap2_asm10_no_0.maf
python3 CompareMafAndCheckMafCoverage.py col_oy.maf minimap2_asm10_oy_0.maf
python3 CompareMafAndCheckMafCoverage.py col_po.maf minimap2_asm10_po_0.maf
python3 CompareMafAndCheckMafCoverage.py col_rsch.maf minimap2_asm10_rsch_4.maf
python3 CompareMafAndCheckMafCoverage.py col_sf.maf minimap2_asm10_sf_2.maf
python3 CompareMafAndCheckMafCoverage.py col_tsu.maf minimap2_asm10_tsu_0.maf
python3 CompareMafAndCheckMafCoverage.py col_wil.maf minimap2_asm10_wil_2.maf
python3 CompareMafAndCheckMafCoverage.py col_ws.maf minimap2_asm10_ws_0.maf
python3 CompareMafAndCheckMafCoverage.py col_wu.maf minimap2_asm10_wu_0.maf
python3 CompareMafAndCheckMafCoverage.py col_zu.maf minimap2_asm10_zu_0.maf
python3 CompareMafAndCheckMafCoverage.py col_bur.maf minimap2_asm20_bur_0.maf
python3 CompareMafAndCheckMafCoverage.py col_can.maf minimap2_asm20_can_0.maf
python3 CompareMafAndCheckMafCoverage.py col_ct.maf minimap2_asm20_ct_1.maf
python3 CompareMafAndCheckMafCoverage.py col_edi.maf minimap2_asm20_edi_0.maf
python3 CompareMafAndCheckMafCoverage.py col_hi.maf minimap2_asm20_hi_0.maf
python3 CompareMafAndCheckMafCoverage.py col_kn.maf minimap2_asm20_kn_0.maf
python3 CompareMafAndCheckMafCoverage.py col_ler.maf minimap2_asm20_ler_0.maf
python3 CompareMafAndCheckMafCoverage.py col_mt.maf minimap2_asm20_mt_0.maf
python3 CompareMafAndCheckMafCoverage.py col_no.maf minimap2_asm20_no_0.maf
python3 CompareMafAndCheckMafCoverage.py col_oy.maf minimap2_asm20_oy_0.maf
python3 CompareMafAndCheckMafCoverage.py col_po.maf minimap2_asm20_po_0.maf
python3 CompareMafAndCheckMafCoverage.py col_rsch.maf minimap2_asm20_rsch_4.maf
python3 CompareMafAndCheckMafCoverage.py col_sf.maf minimap2_asm20_sf_2.maf
python3 CompareMafAndCheckMafCoverage.py col_tsu.maf minimap2_asm20_tsu_0.maf
python3 CompareMafAndCheckMafCoverage.py col_wil.maf minimap2_asm20_wil_2.maf
python3 CompareMafAndCheckMafCoverage.py col_ws.maf minimap2_asm20_ws_0.maf
python3 CompareMafAndCheckMafCoverage.py col_wu.maf minimap2_asm20_wu_0.maf
python3 CompareMafAndCheckMafCoverage.py col_zu.maf minimap2_asm20_zu_0.maf
python3 CompareMafAndCheckMafCoverageAll.py col_bur.maf minimap2_asm5_bur_0.maf
python3 CompareMafAndCheckMafCoverageAll.py col_can.maf minimap2_asm5_can_0.maf
python3 CompareMafAndCheckMafCoverageAll.py col_ct.maf minimap2_asm5_ct_1.maf
python3 CompareMafAndCheckMafCoverageAll.py col_edi.maf minimap2_asm5_edi_0.maf
python3 CompareMafAndCheckMafCoverageAll.py col_hi.maf minimap2_asm5_hi_0.maf
python3 CompareMafAndCheckMafCoverageAll.py col_kn.maf minimap2_asm5_kn_0.maf
python3 CompareMafAndCheckMafCoverageAll.py col_ler.maf minimap2_asm5_ler_0.maf
python3 CompareMafAndCheckMafCoverageAll.py col_mt.maf minimap2_asm5_mt_0.maf
python3 CompareMafAndCheckMafCoverageAll.py col_no.maf minimap2_asm5_no_0.maf
python3 CompareMafAndCheckMafCoverageAll.py col_oy.maf minimap2_asm5_oy_0.maf
python3 CompareMafAndCheckMafCoverageAll.py col_po.maf minimap2_asm5_po_0.maf
python3 CompareMafAndCheckMafCoverageAll.py col_rsch.maf minimap2_asm5_rsch_4.maf
python3 CompareMafAndCheckMafCoverageAll.py col_sf.maf minimap2_asm5_sf_2.maf
python3 CompareMafAndCheckMafCoverageAll.py col_tsu.maf minimap2_asm5_tsu_0.maf
python3 CompareMafAndCheckMafCoverageAll.py col_wil.maf minimap2_asm5_wil_2.maf
python3 CompareMafAndCheckMafCoverageAll.py col_ws.maf minimap2_asm5_ws_0.maf
python3 CompareMafAndCheckMafCoverageAll.py col_wu.maf minimap2_asm5_wu_0.maf
python3 CompareMafAndCheckMafCoverageAll.py col_zu.maf minimap2_asm5_zu_0.maf
python3 CompareMafAndCheckMafCoverageAll.py col_bur.maf minimap2_asm10_bur_0.maf
python3 CompareMafAndCheckMafCoverageAll.py col_can.maf minimap2_asm10_can_0.maf
python3 CompareMafAndCheckMafCoverageAll.py col_ct.maf minimap2_asm10_ct_1.maf
python3 CompareMafAndCheckMafCoverageAll.py col_edi.maf minimap2_asm10_edi_0.maf
python3 CompareMafAndCheckMafCoverageAll.py col_hi.maf minimap2_asm10_hi_0.maf
python3 CompareMafAndCheckMafCoverageAll.py col_kn.maf minimap2_asm10_kn_0.maf
python3 CompareMafAndCheckMafCoverageAll.py col_ler.maf minimap2_asm10_ler_0.maf
python3 CompareMafAndCheckMafCoverageAll.py col_mt.maf minimap2_asm10_mt_0.maf
python3 CompareMafAndCheckMafCoverageAll.py col_no.maf minimap2_asm10_no_0.maf
python3 CompareMafAndCheckMafCoverageAll.py col_oy.maf minimap2_asm10_oy_0.maf
python3 CompareMafAndCheckMafCoverageAll.py col_po.maf minimap2_asm10_po_0.maf
python3 CompareMafAndCheckMafCoverageAll.py col_rsch.maf minimap2_asm10_rsch_4.maf
python3 CompareMafAndCheckMafCoverageAll.py col_sf.maf minimap2_asm10_sf_2.maf
python3 CompareMafAndCheckMafCoverageAll.py col_tsu.maf minimap2_asm10_tsu_0.maf
python3 CompareMafAndCheckMafCoverageAll.py col_wil.maf minimap2_asm10_wil_2.maf
python3 CompareMafAndCheckMafCoverageAll.py col_ws.maf minimap2_asm10_ws_0.maf
python3 CompareMafAndCheckMafCoverageAll.py col_wu.maf minimap2_asm10_wu_0.maf
python3 CompareMafAndCheckMafCoverageAll.py col_zu.maf minimap2_asm10_zu_0.maf
python3 CompareMafAndCheckMafCoverageAll.py col_bur.maf minimap2_asm20_bur_0.maf
python3 CompareMafAndCheckMafCoverageAll.py col_can.maf minimap2_asm20_can_0.maf
python3 CompareMafAndCheckMafCoverageAll.py col_ct.maf minimap2_asm20_ct_1.maf
python3 CompareMafAndCheckMafCoverageAll.py col_edi.maf minimap2_asm20_edi_0.maf
python3 CompareMafAndCheckMafCoverageAll.py col_hi.maf minimap2_asm20_hi_0.maf
python3 CompareMafAndCheckMafCoverageAll.py col_kn.maf minimap2_asm20_kn_0.maf
python3 CompareMafAndCheckMafCoverageAll.py col_ler.maf minimap2_asm20_ler_0.maf
python3 CompareMafAndCheckMafCoverageAll.py col_mt.maf minimap2_asm20_mt_0.maf
python3 CompareMafAndCheckMafCoverageAll.py col_no.maf minimap2_asm20_no_0.maf
python3 CompareMafAndCheckMafCoverageAll.py col_oy.maf minimap2_asm20_oy_0.maf
python3 CompareMafAndCheckMafCoverageAll.py col_po.maf minimap2_asm20_po_0.maf
python3 CompareMafAndCheckMafCoverageAll.py col_rsch.maf minimap2_asm20_rsch_4.maf
python3 CompareMafAndCheckMafCoverageAll.py col_sf.maf minimap2_asm20_sf_2.maf
python3 CompareMafAndCheckMafCoverageAll.py col_tsu.maf minimap2_asm20_tsu_0.maf
python3 CompareMafAndCheckMafCoverageAll.py col_wil.maf minimap2_asm20_wil_2.maf
python3 CompareMafAndCheckMafCoverageAll.py col_ws.maf minimap2_asm20_ws_0.maf
python3 CompareMafAndCheckMafCoverageAll.py col_wu.maf minimap2_asm20_wu_0.maf
python3 CompareMafAndCheckMafCoverageAll.py col_zu.maf minimap2_asm20_zu_0.maf
```
Perform genome alignment using the LAST pipeline
```
# The header of MAF file do not compatible between the LAST pipeline and the chain pipeline.
# We implemented lastToMafComparsion.pl and lastFinalToSplit.pl to reformat the header of MAF files to make them compatible with the used software.
lastdb col tair10.fa
faToTwoBit tair10.fa col.2bit
faSize -detailed tair10.fa > col.size
lastal col bur_0.fa > bur_0_lastal.maf
faSize -detailed bur_0.fa > bur_0.size
faToTwoBit bur_0.fa bur_0.2bit
maf-convert psl bur_0_lastal.maf > bur_0_lastal.psl
axtChain -linearGap=loose -psl bur_0_lastal.psl -faQ -faT tair10.fa bur_0.fa bur_0_lastal.chain
chainMergeSort bur_0_lastal.chain > bur_0_lastal.all.chain
chainPreNet bur_0_lastal.all.chain col.size bur_0.size bur_0_lastal.preNet
chainNet bur_0_lastal.preNet col.size bur_0.size bur_0_lastal.refTarget.net bur_0_lastal.chainNet
netToAxt bur_0_lastal.refTarget.net bur_0_lastal.preNet col.2bit bur_0.2bit stdout | axtSort stdin bur_0_lastal.axt
axtToMaf bur_0_lastal.axt col.size bur_0.size bur_0_lastal_final.maf -qPrefix=query. -tPrefix=col.
perl lastFinalToSplit.pl bur_0_lastal_final.maf > bur_0_lastal_final_forsplit.maf
cat bur_0_lastal.maf | last-split | maf-swap | last-split | maf-swap > bur_0_lastal_split.maf
cat bur_0_lastal_final_forsplit.maf | last-split | maf-swap | last-split | maf-swap > bur_0_lastal_final_split.maf
perl lastToMafComparsion.pl bur_0_lastal_split.maf > bur_0_lastal_split_Comparator.maf
perl lastToMafComparsion.pl bur_0_lastal_final_split.maf > bur_0_lastal_final_split_Comparator.maf
lastal col can_0.fa > can_0_lastal.maf
faSize -detailed can_0.fa > can_0.size
faToTwoBit can_0.fa can_0.2bit
maf-convert psl can_0_lastal.maf > can_0_lastal.psl
axtChain -linearGap=loose -psl can_0_lastal.psl -faQ -faT tair10.fa can_0.fa can_0_lastal.chain
chainMergeSort can_0_lastal.chain > can_0_lastal.all.chain
chainPreNet can_0_lastal.all.chain col.size can_0.size can_0_lastal.preNet
chainNet can_0_lastal.preNet col.size can_0.size can_0_lastal.refTarget.net can_0_lastal.chainNet
netToAxt can_0_lastal.refTarget.net can_0_lastal.preNet col.2bit can_0.2bit stdout | axtSort stdin can_0_lastal.axt
axtToMaf can_0_lastal.axt col.size can_0.size can_0_lastal_final.maf -qPrefix=query. -tPrefix=col.
perl lastFinalToSplit.pl can_0_lastal_final.maf > can_0_lastal_final_forsplit.maf
cat can_0_lastal.maf | last-split | maf-swap | last-split | maf-swap > can_0_lastal_split.maf
cat can_0_lastal_final_forsplit.maf | last-split | maf-swap | last-split | maf-swap > can_0_lastal_final_split.maf
perl lastToMafComparsion.pl can_0_lastal_split.maf > can_0_lastal_split_Comparator.maf
perl lastToMafComparsion.pl can_0_lastal_final_split.maf > can_0_lastal_final_split_Comparator.maf
lastal col ct_1.fa > ct_1_lastal.maf
faSize -detailed ct_1.fa > ct_1.size
faToTwoBit ct_1.fa ct_1.2bit
maf-convert psl ct_1_lastal.maf > ct_1_lastal.psl
axtChain -linearGap=loose -psl ct_1_lastal.psl -faQ -faT tair10.fa ct_1.fa ct_1_lastal.chain
chainMergeSort ct_1_lastal.chain > ct_1_lastal.all.chain
chainPreNet ct_1_lastal.all.chain col.size ct_1.size ct_1_lastal.preNet
chainNet ct_1_lastal.preNet col.size ct_1.size ct_1_lastal.refTarget.net ct_1_lastal.chainNet
netToAxt ct_1_lastal.refTarget.net ct_1_lastal.preNet col.2bit ct_1.2bit stdout | axtSort stdin ct_1_lastal.axt
axtToMaf ct_1_lastal.axt col.size ct_1.size ct_1_lastal_final.maf -qPrefix=query. -tPrefix=col.
perl lastFinalToSplit.pl ct_1_lastal_final.maf > ct_1_lastal_final_forsplit.maf
cat ct_1_lastal.maf | last-split | maf-swap | last-split | maf-swap > ct_1_lastal_split.maf
cat ct_1_lastal_final_forsplit.maf | last-split | maf-swap | last-split | maf-swap > ct_1_lastal_final_split.maf
perl lastToMafComparsion.pl ct_1_lastal_split.maf > ct_1_lastal_split_Comparator.maf
perl lastToMafComparsion.pl ct_1_lastal_final_split.maf > ct_1_lastal_final_split_Comparator.maf
lastal col edi_0.fa > edi_0_lastal.maf
faSize -detailed edi_0.fa > edi_0.size
faToTwoBit edi_0.fa edi_0.2bit
maf-convert psl edi_0_lastal.maf > edi_0_lastal.psl
axtChain -linearGap=loose -psl edi_0_lastal.psl -faQ -faT tair10.fa edi_0.fa edi_0_lastal.chain
chainMergeSort edi_0_lastal.chain > edi_0_lastal.all.chain
chainPreNet edi_0_lastal.all.chain col.size edi_0.size edi_0_lastal.preNet
chainNet edi_0_lastal.preNet col.size edi_0.size edi_0_lastal.refTarget.net edi_0_lastal.chainNet
netToAxt edi_0_lastal.refTarget.net edi_0_lastal.preNet col.2bit edi_0.2bit stdout | axtSort stdin edi_0_lastal.axt
axtToMaf edi_0_lastal.axt col.size edi_0.size edi_0_lastal_final.maf -qPrefix=query. -tPrefix=col.
perl lastFinalToSplit.pl edi_0_lastal_final.maf > edi_0_lastal_final_forsplit.maf
cat edi_0_lastal.maf | last-split | maf-swap | last-split | maf-swap > edi_0_lastal_split.maf
cat edi_0_lastal_final_forsplit.maf | last-split | maf-swap | last-split | maf-swap > edi_0_lastal_final_split.maf
perl lastToMafComparsion.pl edi_0_lastal_split.maf > edi_0_lastal_split_Comparator.maf
perl lastToMafComparsion.pl edi_0_lastal_final_split.maf > edi_0_lastal_final_split_Comparator.maf
lastal col hi_0.fa > hi_0_lastal.maf
faSize -detailed hi_0.fa > hi_0.size
faToTwoBit hi_0.fa hi_0.2bit
maf-convert psl hi_0_lastal.maf > hi_0_lastal.psl
axtChain -linearGap=loose -psl hi_0_lastal.psl -faQ -faT tair10.fa hi_0.fa hi_0_lastal.chain
chainMergeSort hi_0_lastal.chain > hi_0_lastal.all.chain
chainPreNet hi_0_lastal.all.chain col.size hi_0.size hi_0_lastal.preNet
chainNet hi_0_lastal.preNet col.size hi_0.size hi_0_lastal.refTarget.net hi_0_lastal.chainNet
netToAxt hi_0_lastal.refTarget.net hi_0_lastal.preNet col.2bit hi_0.2bit stdout | axtSort stdin hi_0_lastal.axt
axtToMaf hi_0_lastal.axt col.size hi_0.size hi_0_lastal_final.maf -qPrefix=query. -tPrefix=col.
perl lastFinalToSplit.pl hi_0_lastal_final.maf > hi_0_lastal_final_forsplit.maf
cat hi_0_lastal.maf | last-split | maf-swap | last-split | maf-swap > hi_0_lastal_split.maf
cat hi_0_lastal_final_forsplit.maf | last-split | maf-swap | last-split | maf-swap > hi_0_lastal_final_split.maf
perl lastToMafComparsion.pl hi_0_lastal_split.maf > hi_0_lastal_split_Comparator.maf
perl lastToMafComparsion.pl hi_0_lastal_final_split.maf > hi_0_lastal_final_split_Comparator.maf
lastal col kn_0.fa > kn_0_lastal.maf
faSize -detailed kn_0.fa > kn_0.size
faToTwoBit kn_0.fa kn_0.2bit
maf-convert psl kn_0_lastal.maf > kn_0_lastal.psl
axtChain -linearGap=loose -psl kn_0_lastal.psl -faQ -faT tair10.fa kn_0.fa kn_0_lastal.chain
chainMergeSort kn_0_lastal.chain > kn_0_lastal.all.chain
chainPreNet kn_0_lastal.all.chain col.size kn_0.size kn_0_lastal.preNet
chainNet kn_0_lastal.preNet col.size kn_0.size kn_0_lastal.refTarget.net kn_0_lastal.chainNet
netToAxt kn_0_lastal.refTarget.net kn_0_lastal.preNet col.2bit kn_0.2bit stdout | axtSort stdin kn_0_lastal.axt
axtToMaf kn_0_lastal.axt col.size kn_0.size kn_0_lastal_final.maf -qPrefix=query. -tPrefix=col.
perl lastFinalToSplit.pl kn_0_lastal_final.maf > kn_0_lastal_final_forsplit.maf
cat kn_0_lastal.maf | last-split | maf-swap | last-split | maf-swap > kn_0_lastal_split.maf
cat kn_0_lastal_final_forsplit.maf | last-split | maf-swap | last-split | maf-swap > kn_0_lastal_final_split.maf
perl lastToMafComparsion.pl kn_0_lastal_split.maf > kn_0_lastal_split_Comparator.maf
perl lastToMafComparsion.pl kn_0_lastal_final_split.maf > kn_0_lastal_final_split_Comparator.maf
lastal col ler_0.fa > ler_0_lastal.maf
faSize -detailed ler_0.fa > ler_0.size
faToTwoBit ler_0.fa ler_0.2bit
maf-convert psl ler_0_lastal.maf > ler_0_lastal.psl
axtChain -linearGap=loose -psl ler_0_lastal.psl -faQ -faT tair10.fa ler_0.fa ler_0_lastal.chain
chainMergeSort ler_0_lastal.chain > ler_0_lastal.all.chain
chainPreNet ler_0_lastal.all.chain col.size ler_0.size ler_0_lastal.preNet
chainNet ler_0_lastal.preNet col.size ler_0.size ler_0_lastal.refTarget.net ler_0_lastal.chainNet
netToAxt ler_0_lastal.refTarget.net ler_0_lastal.preNet col.2bit ler_0.2bit stdout | axtSort stdin ler_0_lastal.axt
axtToMaf ler_0_lastal.axt col.size ler_0.size ler_0_lastal_final.maf -qPrefix=query. -tPrefix=col.
perl lastFinalToSplit.pl ler_0_lastal_final.maf > ler_0_lastal_final_forsplit.maf
cat ler_0_lastal.maf | last-split | maf-swap | last-split | maf-swap > ler_0_lastal_split.maf
cat ler_0_lastal_final_forsplit.maf | last-split | maf-swap | last-split | maf-swap > ler_0_lastal_final_split.maf
perl lastToMafComparsion.pl ler_0_lastal_split.maf > ler_0_lastal_split_Comparator.maf
perl lastToMafComparsion.pl ler_0_lastal_final_split.maf > ler_0_lastal_final_split_Comparator.maf
lastal col mt_0.fa > mt_0_lastal.maf
faSize -detailed mt_0.fa > mt_0.size
faToTwoBit mt_0.fa mt_0.2bit
maf-convert psl mt_0_lastal.maf > mt_0_lastal.psl
axtChain -linearGap=loose -psl mt_0_lastal.psl -faQ -faT tair10.fa mt_0.fa mt_0_lastal.chain
chainMergeSort mt_0_lastal.chain > mt_0_lastal.all.chain
chainPreNet mt_0_lastal.all.chain col.size mt_0.size mt_0_lastal.preNet
chainNet mt_0_lastal.preNet col.size mt_0.size mt_0_lastal.refTarget.net mt_0_lastal.chainNet
netToAxt mt_0_lastal.refTarget.net mt_0_lastal.preNet col.2bit mt_0.2bit stdout | axtSort stdin mt_0_lastal.axt
axtToMaf mt_0_lastal.axt col.size mt_0.size mt_0_lastal_final.maf -qPrefix=query. -tPrefix=col.
perl lastFinalToSplit.pl mt_0_lastal_final.maf > mt_0_lastal_final_forsplit.maf
cat mt_0_lastal.maf | last-split | maf-swap | last-split | maf-swap > mt_0_lastal_split.maf
cat mt_0_lastal_final_forsplit.maf | last-split | maf-swap | last-split | maf-swap > mt_0_lastal_final_split.maf
perl lastToMafComparsion.pl mt_0_lastal_split.maf > mt_0_lastal_split_Comparator.maf
perl lastToMafComparsion.pl mt_0_lastal_final_split.maf > mt_0_lastal_final_split_Comparator.maf
lastal col no_0.fa > no_0_lastal.maf
faSize -detailed no_0.fa > no_0.size
faToTwoBit no_0.fa no_0.2bit
maf-convert psl no_0_lastal.maf > no_0_lastal.psl
axtChain -linearGap=loose -psl no_0_lastal.psl -faQ -faT tair10.fa no_0.fa no_0_lastal.chain
chainMergeSort no_0_lastal.chain > no_0_lastal.all.chain
chainPreNet no_0_lastal.all.chain col.size no_0.size no_0_lastal.preNet
chainNet no_0_lastal.preNet col.size no_0.size no_0_lastal.refTarget.net no_0_lastal.chainNet
netToAxt no_0_lastal.refTarget.net no_0_lastal.preNet col.2bit no_0.2bit stdout | axtSort stdin no_0_lastal.axt
axtToMaf no_0_lastal.axt col.size no_0.size no_0_lastal_final.maf -qPrefix=query. -tPrefix=col.
perl lastFinalToSplit.pl no_0_lastal_final.maf > no_0_lastal_final_forsplit.maf
cat no_0_lastal.maf | last-split | maf-swap | last-split | maf-swap > no_0_lastal_split.maf
cat no_0_lastal_final_forsplit.maf | last-split | maf-swap | last-split | maf-swap > no_0_lastal_final_split.maf
perl lastToMafComparsion.pl no_0_lastal_split.maf > no_0_lastal_split_Comparator.maf
perl lastToMafComparsion.pl no_0_lastal_final_split.maf > no_0_lastal_final_split_Comparator.maf
lastal col oy_0.fa > oy_0_lastal.maf
faSize -detailed oy_0.fa > oy_0.size
faToTwoBit oy_0.fa oy_0.2bit
maf-convert psl oy_0_lastal.maf > oy_0_lastal.psl
axtChain -linearGap=loose -psl oy_0_lastal.psl -faQ -faT tair10.fa oy_0.fa oy_0_lastal.chain
chainMergeSort oy_0_lastal.chain > oy_0_lastal.all.chain
chainPreNet oy_0_lastal.all.chain col.size oy_0.size oy_0_lastal.preNet
chainNet oy_0_lastal.preNet col.size oy_0.size oy_0_lastal.refTarget.net oy_0_lastal.chainNet
netToAxt oy_0_lastal.refTarget.net oy_0_lastal.preNet col.2bit oy_0.2bit stdout | axtSort stdin oy_0_lastal.axt
axtToMaf oy_0_lastal.axt col.size oy_0.size oy_0_lastal_final.maf -qPrefix=query. -tPrefix=col.
perl lastFinalToSplit.pl oy_0_lastal_final.maf > oy_0_lastal_final_forsplit.maf
cat oy_0_lastal.maf | last-split | maf-swap | last-split | maf-swap > oy_0_lastal_split.maf
cat oy_0_lastal_final_forsplit.maf | last-split | maf-swap | last-split | maf-swap > oy_0_lastal_final_split.maf
perl lastToMafComparsion.pl oy_0_lastal_split.maf > oy_0_lastal_split_Comparator.maf
perl lastToMafComparsion.pl oy_0_lastal_final_split.maf > oy_0_lastal_final_split_Comparator.maf
lastal col po_0.fa > po_0_lastal.maf
faSize -detailed po_0.fa > po_0.size
faToTwoBit po_0.fa po_0.2bit
maf-convert psl po_0_lastal.maf > po_0_lastal.psl
axtChain -linearGap=loose -psl po_0_lastal.psl -faQ -faT tair10.fa po_0.fa po_0_lastal.chain
chainMergeSort po_0_lastal.chain > po_0_lastal.all.chain
chainPreNet po_0_lastal.all.chain col.size po_0.size po_0_lastal.preNet
chainNet po_0_lastal.preNet col.size po_0.size po_0_lastal.refTarget.net po_0_lastal.chainNet
netToAxt po_0_lastal.refTarget.net po_0_lastal.preNet col.2bit po_0.2bit stdout | axtSort stdin po_0_lastal.axt
axtToMaf po_0_lastal.axt col.size po_0.size po_0_lastal_final.maf -qPrefix=query. -tPrefix=col.
perl lastFinalToSplit.pl po_0_lastal_final.maf > po_0_lastal_final_forsplit.maf
cat po_0_lastal.maf | last-split | maf-swap | last-split | maf-swap > po_0_lastal_split.maf
cat po_0_lastal_final_forsplit.maf | last-split | maf-swap | last-split | maf-swap > po_0_lastal_final_split.maf
perl lastToMafComparsion.pl po_0_lastal_split.maf > po_0_lastal_split_Comparator.maf
perl lastToMafComparsion.pl po_0_lastal_final_split.maf > po_0_lastal_final_split_Comparator.maf
lastal col rsch_4.fa > rsch_4_lastal.maf
faSize -detailed rsch_4.fa > rsch_4.size
faToTwoBit rsch_4.fa rsch_4.2bit
maf-convert psl rsch_4_lastal.maf > rsch_4_lastal.psl
axtChain -linearGap=loose -psl rsch_4_lastal.psl -faQ -faT tair10.fa rsch_4.fa rsch_4_lastal.chain
chainMergeSort rsch_4_lastal.chain > rsch_4_lastal.all.chain
chainPreNet rsch_4_lastal.all.chain col.size rsch_4.size rsch_4_lastal.preNet
chainNet rsch_4_lastal.preNet col.size rsch_4.size rsch_4_lastal.refTarget.net rsch_4_lastal.chainNet
netToAxt rsch_4_lastal.refTarget.net rsch_4_lastal.preNet col.2bit rsch_4.2bit stdout | axtSort stdin rsch_4_lastal.axt
axtToMaf rsch_4_lastal.axt col.size rsch_4.size rsch_4_lastal_final.maf -qPrefix=query. -tPrefix=col.
perl lastFinalToSplit.pl rsch_4_lastal_final.maf > rsch_4_lastal_final_forsplit.maf
cat rsch_4_lastal.maf | last-split | maf-swap | last-split | maf-swap > rsch_4_lastal_split.maf
cat rsch_4_lastal_final_forsplit.maf | last-split | maf-swap | last-split | maf-swap > rsch_4_lastal_final_split.maf
perl lastToMafComparsion.pl rsch_4_lastal_split.maf > rsch_4_lastal_split_Comparator.maf
perl lastToMafComparsion.pl rsch_4_lastal_final_split.maf > rsch_4_lastal_final_split_Comparator.maf
lastal col sf_2.fa > sf_2_lastal.maf
faSize -detailed sf_2.fa > sf_2.size
faToTwoBit sf_2.fa sf_2.2bit
maf-convert psl sf_2_lastal.maf > sf_2_lastal.psl
axtChain -linearGap=loose -psl sf_2_lastal.psl -faQ -faT tair10.fa sf_2.fa sf_2_lastal.chain
chainMergeSort sf_2_lastal.chain > sf_2_lastal.all.chain
chainPreNet sf_2_lastal.all.chain col.size sf_2.size sf_2_lastal.preNet
chainNet sf_2_lastal.preNet col.size sf_2.size sf_2_lastal.refTarget.net sf_2_lastal.chainNet
netToAxt sf_2_lastal.refTarget.net sf_2_lastal.preNet col.2bit sf_2.2bit stdout | axtSort stdin sf_2_lastal.axt
axtToMaf sf_2_lastal.axt col.size sf_2.size sf_2_lastal_final.maf -qPrefix=query. -tPrefix=col.
perl lastFinalToSplit.pl sf_2_lastal_final.maf > sf_2_lastal_final_forsplit.maf
cat sf_2_lastal.maf | last-split | maf-swap | last-split | maf-swap > sf_2_lastal_split.maf
cat sf_2_lastal_final_forsplit.maf | last-split | maf-swap | last-split | maf-swap > sf_2_lastal_final_split.maf
perl lastToMafComparsion.pl sf_2_lastal_split.maf > sf_2_lastal_split_Comparator.maf
perl lastToMafComparsion.pl sf_2_lastal_final_split.maf > sf_2_lastal_final_split_Comparator.maf
lastal col tsu_0.fa > tsu_0_lastal.maf
faSize -detailed tsu_0.fa > tsu_0.size
faToTwoBit tsu_0.fa tsu_0.2bit
maf-convert psl tsu_0_lastal.maf > tsu_0_lastal.psl
axtChain -linearGap=loose -psl tsu_0_lastal.psl -faQ -faT tair10.fa tsu_0.fa tsu_0_lastal.chain
chainMergeSort tsu_0_lastal.chain > tsu_0_lastal.all.chain
chainPreNet tsu_0_lastal.all.chain col.size tsu_0.size tsu_0_lastal.preNet
chainNet tsu_0_lastal.preNet col.size tsu_0.size tsu_0_lastal.refTarget.net tsu_0_lastal.chainNet
netToAxt tsu_0_lastal.refTarget.net tsu_0_lastal.preNet col.2bit tsu_0.2bit stdout | axtSort stdin tsu_0_lastal.axt
axtToMaf tsu_0_lastal.axt col.size tsu_0.size tsu_0_lastal_final.maf -qPrefix=query. -tPrefix=col.
perl lastFinalToSplit.pl tsu_0_lastal_final.maf > tsu_0_lastal_final_forsplit.maf
cat tsu_0_lastal.maf | last-split | maf-swap | last-split | maf-swap > tsu_0_lastal_split.maf
cat tsu_0_lastal_final_forsplit.maf | last-split | maf-swap | last-split | maf-swap > tsu_0_lastal_final_split.maf
perl lastToMafComparsion.pl tsu_0_lastal_split.maf > tsu_0_lastal_split_Comparator.maf
perl lastToMafComparsion.pl tsu_0_lastal_final_split.maf > tsu_0_lastal_final_split_Comparator.maf
lastal col wil_2.fa > wil_2_lastal.maf
faSize -detailed wil_2.fa > wil_2.size
faToTwoBit wil_2.fa wil_2.2bit
maf-convert psl wil_2_lastal.maf > wil_2_lastal.psl
axtChain -linearGap=loose -psl wil_2_lastal.psl -faQ -faT tair10.fa wil_2.fa wil_2_lastal.chain
chainMergeSort wil_2_lastal.chain > wil_2_lastal.all.chain
chainPreNet wil_2_lastal.all.chain col.size wil_2.size wil_2_lastal.preNet
chainNet wil_2_lastal.preNet col.size wil_2.size wil_2_lastal.refTarget.net wil_2_lastal.chainNet
netToAxt wil_2_lastal.refTarget.net wil_2_lastal.preNet col.2bit wil_2.2bit stdout | axtSort stdin wil_2_lastal.axt
axtToMaf wil_2_lastal.axt col.size wil_2.size wil_2_lastal_final.maf -qPrefix=query. -tPrefix=col.
perl lastFinalToSplit.pl wil_2_lastal_final.maf > wil_2_lastal_final_forsplit.maf
cat wil_2_lastal.maf | last-split | maf-swap | last-split | maf-swap > wil_2_lastal_split.maf
cat wil_2_lastal_final_forsplit.maf | last-split | maf-swap | last-split | maf-swap > wil_2_lastal_final_split.maf
perl lastToMafComparsion.pl wil_2_lastal_split.maf > wil_2_lastal_split_Comparator.maf
perl lastToMafComparsion.pl wil_2_lastal_final_split.maf > wil_2_lastal_final_split_Comparator.maf
lastal col ws_0.fa > ws_0_lastal.maf
faSize -detailed ws_0.fa > ws_0.size
faToTwoBit ws_0.fa ws_0.2bit
maf-convert psl ws_0_lastal.maf > ws_0_lastal.psl
axtChain -linearGap=loose -psl ws_0_lastal.psl -faQ -faT tair10.fa ws_0.fa ws_0_lastal.chain
chainMergeSort ws_0_lastal.chain > ws_0_lastal.all.chain
chainPreNet ws_0_lastal.all.chain col.size ws_0.size ws_0_lastal.preNet
chainNet ws_0_lastal.preNet col.size ws_0.size ws_0_lastal.refTarget.net ws_0_lastal.chainNet
netToAxt ws_0_lastal.refTarget.net ws_0_lastal.preNet col.2bit ws_0.2bit stdout | axtSort stdin ws_0_lastal.axt
axtToMaf ws_0_lastal.axt col.size ws_0.size ws_0_lastal_final.maf -qPrefix=query. -tPrefix=col.
perl lastFinalToSplit.pl ws_0_lastal_final.maf > ws_0_lastal_final_forsplit.maf
cat ws_0_lastal.maf | last-split | maf-swap | last-split | maf-swap > ws_0_lastal_split.maf
cat ws_0_lastal_final_forsplit.maf | last-split | maf-swap | last-split | maf-swap > ws_0_lastal_final_split.maf
perl lastToMafComparsion.pl ws_0_lastal_split.maf > ws_0_lastal_split_Comparator.maf
perl lastToMafComparsion.pl ws_0_lastal_final_split.maf > ws_0_lastal_final_split_Comparator.maf
lastal col wu_0.fa > wu_0_lastal.maf
faSize -detailed wu_0.fa > wu_0.size
faToTwoBit wu_0.fa wu_0.2bit
maf-convert psl wu_0_lastal.maf > wu_0_lastal.psl
axtChain -linearGap=loose -psl wu_0_lastal.psl -faQ -faT tair10.fa wu_0.fa wu_0_lastal.chain
chainMergeSort wu_0_lastal.chain > wu_0_lastal.all.chain
chainPreNet wu_0_lastal.all.chain col.size wu_0.size wu_0_lastal.preNet
chainNet wu_0_lastal.preNet col.size wu_0.size wu_0_lastal.refTarget.net wu_0_lastal.chainNet
netToAxt wu_0_lastal.refTarget.net wu_0_lastal.preNet col.2bit wu_0.2bit stdout | axtSort stdin wu_0_lastal.axt
axtToMaf wu_0_lastal.axt col.size wu_0.size wu_0_lastal_final.maf -qPrefix=query. -tPrefix=col.
perl lastFinalToSplit.pl wu_0_lastal_final.maf > wu_0_lastal_final_forsplit.maf
cat wu_0_lastal.maf | last-split | maf-swap | last-split | maf-swap > wu_0_lastal_split.maf
cat wu_0_lastal_final_forsplit.maf | last-split | maf-swap | last-split | maf-swap > wu_0_lastal_final_split.maf
perl lastToMafComparsion.pl wu_0_lastal_split.maf > wu_0_lastal_split_Comparator.maf
perl lastToMafComparsion.pl wu_0_lastal_final_split.maf > wu_0_lastal_final_split_Comparator.maf
lastal col zu_0.fa > zu_0_lastal.maf
faSize -detailed zu_0.fa > zu_0.size
faToTwoBit zu_0.fa zu_0.2bit
maf-convert psl zu_0_lastal.maf > zu_0_lastal.psl
axtChain -linearGap=loose -psl zu_0_lastal.psl -faQ -faT tair10.fa zu_0.fa zu_0_lastal.chain
chainMergeSort zu_0_lastal.chain > zu_0_lastal.all.chain
chainPreNet zu_0_lastal.all.chain col.size zu_0.size zu_0_lastal.preNet
chainNet zu_0_lastal.preNet col.size zu_0.size zu_0_lastal.refTarget.net zu_0_lastal.chainNet
netToAxt zu_0_lastal.refTarget.net zu_0_lastal.preNet col.2bit zu_0.2bit stdout | axtSort stdin zu_0_lastal.axt
axtToMaf zu_0_lastal.axt col.size zu_0.size zu_0_lastal_final.maf -qPrefix=query. -tPrefix=col.
perl lastFinalToSplit.pl zu_0_lastal_final.maf > zu_0_lastal_final_forsplit.maf
cat zu_0_lastal.maf | last-split | maf-swap | last-split | maf-swap > zu_0_lastal_split.maf
cat zu_0_lastal_final_forsplit.maf | last-split | maf-swap | last-split | maf-swap > zu_0_lastal_final_split.maf
perl lastToMafComparsion.pl zu_0_lastal_split.maf > zu_0_lastal_split_Comparator.maf
perl lastToMafComparsion.pl zu_0_lastal_final_split.maf > zu_0_lastal_final_split_Comparator.maf
/usr/bin/time -v bash last_bur_0.sh > last_bur_0.log 2>&1
/usr/bin/time -v bash last_can_0.sh > last_can_0.log 2>&1
/usr/bin/time -v bash last_ct_1.sh > last_ct_1.log 2>&1
/usr/bin/time -v bash last_edi_0.sh > last_edi_0.log 2>&1
/usr/bin/time -v bash last_hi_0.sh > last_hi_0.log 2>&1
/usr/bin/time -v bash last_kn_0.sh > last_kn_0.log 2>&1
/usr/bin/time -v bash last_ler_0.sh > last_ler_0.log 2>&1
/usr/bin/time -v bash last_mt_0.sh > last_mt_0.log 2>&1
/usr/bin/time -v bash last_no_0.sh > last_no_0.log 2>&1
/usr/bin/time -v bash last_oy_0.sh > last_oy_0.log 2>&1
/usr/bin/time -v bash last_po_0.sh > last_po_0.log 2>&1
/usr/bin/time -v bash last_rsch_4.sh > last_rsch_4.log 2>&1
/usr/bin/time -v bash last_sf_2.sh > last_sf_2.log 2>&1
/usr/bin/time -v bash last_tsu_0.sh > last_tsu_0.log 2>&1
/usr/bin/time -v bash last_wil_2.sh > last_wil_2.log 2>&1
/usr/bin/time -v bash last_ws_0.sh > last_ws_0.log 2>&1
/usr/bin/time -v bash last_wu_0.sh > last_wu_0.log 2>&1
/usr/bin/time -v bash last_zu_0.sh > last_zu_0.log 2>&1
```
Evaluate LAST one-to-one alignments
```
python3 CompareMafAndCheckMafCoverage.py col_bur.maf bur_0_lastal_split_Comparator.maf
python3 CompareMafAndCheckMafCoverage.py col_can.maf can_0_lastal_split_Comparator.maf
python3 CompareMafAndCheckMafCoverage.py col_ct.maf ct_1_lastal_split_Comparator.maf
python3 CompareMafAndCheckMafCoverage.py col_edi.maf edi_0_lastal_split_Comparator.maf
python3 CompareMafAndCheckMafCoverage.py col_hi.maf hi_0_lastal_split_Comparator.maf
python3 CompareMafAndCheckMafCoverage.py col_kn.maf kn_0_lastal_split_Comparator.maf
python3 CompareMafAndCheckMafCoverage.py col_ler.maf ler_0_lastal_split_Comparator.maf
python3 CompareMafAndCheckMafCoverage.py col_mt.maf mt_0_lastal_split_Comparator.maf
python3 CompareMafAndCheckMafCoverage.py col_no.maf no_0_lastal_split_Comparator.maf
python3 CompareMafAndCheckMafCoverage.py col_oy.maf oy_0_lastal_split_Comparator.maf
python3 CompareMafAndCheckMafCoverage.py col_po.maf po_0_lastal_split_Comparator.maf
python3 CompareMafAndCheckMafCoverage.py col_rsch.maf rsch_4_lastal_split_Comparator.maf
python3 CompareMafAndCheckMafCoverage.py col_sf.maf sf_2_lastal_split_Comparator.maf
python3 CompareMafAndCheckMafCoverage.py col_tsu.maf tsu_0_lastal_split_Comparator.maf
python3 CompareMafAndCheckMafCoverage.py col_wil.maf wil_2_lastal_split_Comparator.maf
python3 CompareMafAndCheckMafCoverage.py col_ws.maf ws_0_lastal_split_Comparator.maf
python3 CompareMafAndCheckMafCoverage.py col_wu.maf wu_0_lastal_split_Comparator.maf
python3 CompareMafAndCheckMafCoverage.py col_zu.maf zu_0_lastal_split_Comparator.maf
python3 CompareMafAndCheckMafCoverage.py col_bur.maf bur_0_lastal_final_split_Comparator.maf
python3 CompareMafAndCheckMafCoverage.py col_can.maf can_0_lastal_final_split_Comparator.maf
python3 CompareMafAndCheckMafCoverage.py col_ct.maf ct_1_lastal_final_split_Comparator.maf
python3 CompareMafAndCheckMafCoverage.py col_edi.maf edi_0_lastal_final_split_Comparator.maf
python3 CompareMafAndCheckMafCoverage.py col_hi.maf hi_0_lastal_final_split_Comparator.maf
python3 CompareMafAndCheckMafCoverage.py col_kn.maf kn_0_lastal_final_split_Comparator.maf
python3 CompareMafAndCheckMafCoverage.py col_ler.maf ler_0_lastal_final_split_Comparator.maf
python3 CompareMafAndCheckMafCoverage.py col_mt.maf mt_0_lastal_final_split_Comparator.maf
python3 CompareMafAndCheckMafCoverage.py col_no.maf no_0_lastal_final_split_Comparator.maf
python3 CompareMafAndCheckMafCoverage.py col_oy.maf oy_0_lastal_final_split_Comparator.maf
python3 CompareMafAndCheckMafCoverage.py col_po.maf po_0_lastal_final_split_Comparator.maf
python3 CompareMafAndCheckMafCoverage.py col_rsch.maf rsch_4_lastal_final_split_Comparator.maf
python3 CompareMafAndCheckMafCoverage.py col_sf.maf sf_2_lastal_final_split_Comparator.maf
python3 CompareMafAndCheckMafCoverage.py col_tsu.maf tsu_0_lastal_final_split_Comparator.maf
python3 CompareMafAndCheckMafCoverage.py col_wil.maf wil_2_lastal_final_split_Comparator.maf
python3 CompareMafAndCheckMafCoverage.py col_ws.maf ws_0_lastal_final_split_Comparator.maf
python3 CompareMafAndCheckMafCoverage.py col_wu.maf wu_0_lastal_final_split_Comparator.maf
python3 CompareMafAndCheckMafCoverage.py col_zu.maf zu_0_lastal_final_split_Comparator.maf