QUAST stands for QUality ASsessment Tool. The tool evaluates genome assemblies by computing various metrics. The package includes the general QUAST tool for genome assemblies, MetaQUAST, the extension for metagenomic datasets, and Icarus, interactive visualizer for these tools.

References:

• Alla Mikheenko, Andrey Prjibelski, Vladislav Saveliev, Dmitry Antipov, Alexey Gurevich, Versatile genome assembly evaluation with QUAST-LG, Bioinformatics (2018) 34 (13): i142-i150. doi: 10.1093/bioinformatics/bty266 First published online: June 27, 2018
• Alla Mikheenko, Gleb Valin, Andrey Prjibelski, Vladislav Saveliev, Alexey Gurevich, Icarus: visualizer for de novo assembly evaluation, Bioinformatics (2016). doi: 10.1093/bioinformatics/btw379 First published online: July 4, 2016
• Alla Mikheenko, Vladislav Saveliev, Alexey Gurevich, MetaQUAST: evaluation of metagenome assemblies, Bioinformatics (2016) 32 (7): 1088-1090. doi: 10.1093/bioinformatics/btv697 First published online: November 26, 2015
• Alexey Gurevich, Vladislav Saveliev, Nikolay Vyahhi and Glenn Tesler, QUAST: quality assessment tool for genome assemblies, Bioinformatics (2013) 29 (8): 1072-1075. doi: 10.1093/bioinformatics/btt086 First published online: February 19, 2013

• QUAST Main Site

• Module Name: quast (see the modules page for more information)
• This application produces HTML reports. You can use hpcdrive to view these reports on your local workstation.
• Environment variables set
  • QUAST_HOME
• Example files in $QUAST_HOME/test_data

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf]$ sinteractive --gres lscratch:10
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load quast
[+] Loading quast, version 5.0.2...
[user@cn3144 ~]$ cd /lscratch/$SLURM_JOB_ID
[user@cn3144 ~]$ quast.py --threads 2 \
    $QUAST_HOME/test_data/contigs_{1,2}.fasta \
    -R $QUAST_HOME/test_data/reference.fasta.gz \
    -G $QUAST_HOME/test_data/genes.gff 

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. quast.sh). For example:

#!/bin/bash
set -e
module load quast

test -n "$SLURM_CPUS_PER_TASK" || SLURM_CPUS_PER_TASK=2

quast.py --threads $SLURM_CPUS_PER_TASK \
    $QUAST_HOME/test_data/contigs_{1,2}.fasta \
    -R $QUAST_HOME/test_data/reference.fasta.gz \
    -G $QUAST_HOME/test_data/genes.gff

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#] quast.sh

Create a swarmfile (e.g. quast.swarm). For example:

quast.py $QUAST_HOME/test_data/contigs_{1,2}.fasta \
         -R $QUAST_HOME/test_data/reference.fasta.gz \
         -G $QUAST_HOME/test_data/genes.gff
quast.py $QUAST_HOME/test_data/contigs_{1,2}.fasta \
         -R $QUAST_HOME/test_data/reference.fasta.gz \
         -G $QUAST_HOME/test_data/genes.gff
quast.py $QUAST_HOME/test_data/contigs_{1,2}.fasta \
         -R $QUAST_HOME/test_data/reference.fasta.gz \
         -G $QUAST_HOME/test_data/genes.gff

Submit this job using the swarm command.

swarm -f quast.swarm [-g #] -t # --module quast