The scripts we used for assembling and comparing of de novo assemblies project.
The E. pauciflora genome project was deposited at NCBI under BioProject number PRJNA450887.
The whole genome sequencing data are available in the Sequence Read Archive with accession number SRR7153044-SRR7153116.
The pipeline for different assemblies assessment is available in https://github.com/asdcid/Genome_Assembly_Assessment
- Fastqc
- Bbduk v37.31
- Porechop v0.2.1
- Nanofilt v1.2.0
- GenomeScope
- SGA-preqc
- Jellyfish v1.1.12
- Canu v1.6, v1.7
- Flye v2.3.5
- Marvel v1.0
- MaSuRCA v3.2.6
- BLASTN v2.7.1+
- Blobtools
- Ngmlr v0.2.6
- BUSCO v3.0.2
- Bowtie2 v2.2.6
- Quast
- samtools v1.5
- Mummer v4.0beta2
- Racon
- Pilon v1.22
- Qualimap v2.2.1
- Purge Haplotigs
- Sniffles
- CGAL
- LTR_retriever
- GenomeTools
- Ltr_finder
- RepeatMasker v4.0.7
- RepeatModeler v1.0.11
- python2.7 or higher