quast

Genetics

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 .


Info

Module Name

quast

Last Updated On

08/29/2023

Support Level

Primary Support

Software Access Level

Open Access

Home Page

http://sourceforge.net/projects/quast/

Documentation

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 .

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 small,large,ram256g,ram1t
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

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

Agate Modules

Default

4.3

Other Modules

4.3, 4.6.3, 5.0.0, 5.2.0

Mangi Modules

Default

4.3

Other Modules

4.3, 4.6.3, 5.0.0, 5.2.0

Mesabi Modules

Default

4.3

Other Modules

4.3, 4.6.3, 5.0.0, 5.2.0