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QUAST

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:

There may be multiple versions of QUAST available. An easy way of selecting the version is to use modules. To see the modules available, type

module avail quast

To select a module, type

module load quast/[ver]

where [ver] is the version of choice.

Environment variables set:

On Helix

Sample session:

module load quast
cd /data/teacher
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
You can view the HTML report of the results from your local machine by pointing Firefox to: sftp://helix.nih.gov/data/teacher/quast_results/latest/report.html
Batch job on Biowulf

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

#!/bin/bash
module load quast
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 Slurm sbatch command.

sbatch --cpus-per-task=1 quast.sh
Swarm of Jobs on Biowulf

Create a swarmfile (e.g. template.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 --module quast
Interactive job on Biowulf
Sample session:
sinteractive
module load quast
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
Documentation