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 default 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¶
Serial job¶
Here is an example job running on 1 core and 1GB of memory, using the QUAST test data:
#!/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}