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Quast

Introduction ~~~~~~~~ Quast is Quality Assessment Tool for Genome Assemblies.

Note: Running QUAST, please use the command: quast.py| metaquast.py fastafile [OTHER OPTIONS] DO NOT call it 'python quast.py| metaquast.py'

For more information, please check its website: https://biocontainers.pro/tools/quast and its home page on Github.

Versions

  • 5.0.2
  • 5.2.0

Commands ~~~~~~~ - quast.py - metaquast.py

Module

You can load the modules by:

module load biocontainers
module load quast

Example job ~~~~~ .. warning:: Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run Quast on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name 
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 8
#SBATCH --job-name=quast
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers quast

metaquast.py  --gene-finding --threads 8  \ 
    meta_contigs_1.fasta meta_contigs_2.fasta \
    -r meta_ref_1.fasta,meta_ref_2.fasta,meta_ref_3.fasta \
    -o quast_out_genefinding