Rnaquast

Introduction

Rnaquast is a quality assessment tool for de novo transcriptome assemblies.

For more information, please check its website: https://biocontainers.pro/tools/rnaquast and its home page: http://cab.spbu.ru/software/rnaquast/.

Versions

2.2.1

Commands

rnaQUAST.py

Module

You can load the modules by:

module load biocontainers
module load rnaquast

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 Rnaquast on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 12
#SBATCH --job-name=rnaquast
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers rnaquast

rnaQUAST.py -t 12 -o output \
     --transcripts test_data/Trinity.fasta test_data/idba.fasta \
     --reference test_data/Saccharomyces_cerevisiae.R64-1-1.75.dna.toplevel.fa \
     --gtf test_data/Saccharomyces_cerevisiae.R64-1-1.75.gtf