quast

Summary

• Module Name: quast

• Support Level: Primary Support

• Software Access Level: Open Access

• Home Page: http://sourceforge.net/projects/quast/

Software Description

QUAST stands for QUality ASsesment Tool. The tool evaluates genome assemblies by computing various metrics. You can find all project news at http://sourceforge.net/projects/quast .

General Linux

To load this module for use in a Linux environment, you can run the command:

module load quast

Depending on where you are working, there may be more than one version of quast available. To see which modules are available for loading you can run:

module avail quast

Slurm Example

#!/bin/bash
#SBATCH --job-name="rfm_RunQUASTTest_job"
#SBATCH --ntasks=1
#SBATCH --ntasks-per-node=1
#SBATCH --output=rfm_RunQUASTTest_job.out
#SBATCH --error=rfm_RunQUASTTest_job.err
#SBATCH --time=0:10:0
#SBATCH -p msismall
module load quast/4.3
wget https://public.s3.msi.umn.edu/reframe/sw/quast/contigs_1.fasta
wget https://public.s3.msi.umn.edu/reframe/sw/quast/contigs_2.fasta
wget https://public.s3.msi.umn.edu/reframe/sw/quast/genes.gff
wget https://public.s3.msi.umn.edu/reframe/sw/quast/reference.fasta.gz
quast contigs_1.fasta contigs_2.fasta -R reference.fasta.gz -G genes.gff -o output