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Mumer_alignment
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This script is used for anignment between differenr genomes. As the published VdLs.17 genome is the represent for V.dahliae race 2 strains, it ia used for alignment of our 5 race 2 strains.
#Promer alignment of Assemblies
##against 12008 genome
MUMmer was run to align assemblies against the reference genome.
```bash
Reference=assembly/merged_canu_spades/V.dahliae/Ls17/ensembl/Verticillium_dahliae.ASM15067v2.dna.toplevel.fa
#Query=repeat_masked/V.dahliae/12008/ncbi_filtered_contigs_repmask/12008_contigs_unmasked.fa
#Query=repeat_masked/V.dahliae/61/ncbi_filter_contigs/*_contigs_unmasked.fa
Query=assembly/spades_pacbio/V.dahliae/12008/filtered_contigs/contigs_min_500bp.fasta
Strain=$(echo $Query | rev | cut -f3 -d '/' | rev)
Organism=$(echo $Query | rev | cut -f4 -d '/' | rev)
echo "$Organism - $Strain"
Prefix="$Strain"_vs_Ls17
OutDir=analysis/genome_alignment/mummer/$Organism/$Strain/$Prefix
ProgDir=/home/fanron/git_repos/tools/seq_tools/genome_alignment/promer
qsub $ProgDir/sub_MUMmer.sh $Reference $Query $Prefix $OutDir
```
```
## Aganist JR2 PacBio genome.
```bash
Reference=assembly/merged_canu_spades/V.dahliae/JR2/ensembl/Verticillium_dahliaejr2.GCA_000400815.2.dna.toplevel.fa
Query=repeat_masked/V.dahliae/12008/ncbi_filtered_contigs_repmask/12008_contigs_unmasked.fa
Strain=$(echo $Query | rev | cut -f3 -d '/' | rev)
Organism=$(echo $Query | rev | cut -f4 -d '/' | rev)
echo "$Organism - $Strain"
Prefix="$Strain"_vs_JR2_after_ncbi
OutDir=analysis/genome_alignment/mummer/$Organism/$Strain/$Prefix
ProgDir=/home/fanron/git_repos/tools/seq_tools/genome_alignment/promer
qsub $ProgDir/sub_MUMmer.sh $Reference $Query $Prefix $OutDir
```
Reference=assembly/merged_canu_spades/V.dahliae/JR2/ensembl/Verticillium_dahliaejr2.GCA_000400815.2.dna.toplevel.fa
#Query=repeat_masked/V.dahliae/12008/ncbi_filtered_contigs_repmask/12008_contigs_unmasked.fa
#Query=repeat_masked/V.dahliae/61/ncbi_filter_contigs/*_contigs_unmasked.fa
Query=assembly/spades/V.dahliae/61/ncbi_edits/contigs_min_500bp.fasta
Strain=$(echo $Query | rev | cut -f3 -d '/' | rev)
Organism=$(echo $Query | rev | cut -f4 -d '/' | rev)
echo "$Organism - $Strain"
Prefix="$Strain"_vs_JR2
OutDir=analysis/genome_alignment/mummer/$Organism/$Strain/$Prefix
ProgDir=/home/fanron/git_repos/tools/seq_tools/genome_alignment/promer
qsub $ProgDir/sub_MUMmer.sh $Reference $Query $Prefix $OutDir
## Align 51,53,58,61 genome aganist 12008 genome
Reference=repeat_masked/V.dahliae/12008/ncbi_filtered_contigs_repmask/12008_contigs_unmasked.fa
Query=repeat_masked/V.dahliae/58/ncbi_filter_contigs/*_contigs_unmasked.fa
Strain=$(echo $Query | rev | cut -f3 -d '/' | rev)
Organism=$(echo $Query | rev | cut -f4 -d '/' | rev)
echo "$Organism - $Strain"
Prefix="$Strain"_vs_J12008_after_ncbi
OutDir=analysis/genome_alignment/mummer/$Organism/$Strain/$Prefix
ProgDir=/home/fanron/git_repos/tools/seq_tools/genome_alignment/promer
qsub $ProgDir/sub_MUMmer.sh $Reference $Query $Prefix $OutDir