Main tool: QUAST
Code repository: https://github.com/ablab/quast
Additional tools:
- gridss: 1.4.1
Basic information on how to use this tool:
- executable: quast.py
- help: --help
- version: --version
- description: Genome assembly evaluation tool
Additional information:
You need a license key if you want to use GeneMark with Quast!
The key can be downloaded from http://exon.gatech.edu/GeneMark/license_download.cgi page (GeneMark is free for non-commercial use).
You should choose GeneMarkS-T LINUX 64. Download your license key and add it to your data folder or another folder you will bind to the container. Inside the container, copy the key to your home folder.
cp /data/gm_key_64 ~/.gm_key
Full documentation: https://quast.sourceforge.net/docs/manual.html
# basic statistics without reference
quast.py contigs.fasta
# genome evaluation with reference
quast.py contigs.fasta -r reference.fasta.gz -g genes.gff
# metagenomic assemblies
metaquast.py contigs_1 contigs_2 ... -r reference_1,reference_2,reference_3,...