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QUAST

QUality ASsessment Tool for Genome Assemblies (QUAST) evaluates genomes from multiple assemblies for comparison.

QUAST is available as a module on Apocrita.

Usage

To run the latest installed version of QUAST, simply load the quast module:

$ module load quast
$ quast.py --help

Usage: quast.py [options] <files_with_contigs>

Options:
-o  --output-dir  <dirname>   Directory to store all result files
-R                <filename>  Reference genome file
-G  --genes       <filename>  File with gene coordinates in the reference
-O  --operons     <filename>  File with operon coordinates in the reference
-m  --min-contig  <int>       Lower threshold for contig length
-t  --threads     <int>       Maximum number of threads

For usage documentation, run quast.py --help.

GeneMark Licensing

An individual, free academic license is required if using GeneMark; QUAST will produce a warning message if GeneMark functionality is used without obtaining a license from here beforehand. Please select the GeneMarkS and LINUX 64 options and complete the remaining of the form with your personal details.

Example job

Here is an example job using the QUAST test data, running on 1 core and 1GB of memory:

#!/bin/bash
#$ -cwd
#$ -j y
#$ -pe smp 1
#$ -l h_rt=1:0:0
#$ -l h_vmem=1G

module load quast

# Set the path for the test_data directory
# Replace <VERSION> with the actual application version number
BASE_URL=/share/apps/centos7/quast/<VERSION>/test_data

quast.py ${BASE_URL}/contigs_1.fasta \
         ${BASE_URL}/contigs_2.fasta \
         -R ${BASE_URL}/reference.fasta.gz \
         -G ${BASE_URL}/genes.gff \
         -t ${NSLOTS}

References