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

Dependencies de novo quality assessment and read alignment

Note

When reference genome and gene database are unavailable, users can also use BUSCO and GeneMarkS-T in rnaQUAST pipeline. Since GeneMarkS-T requires the license key, users may need to download your own key, and put it in your $HOME. rnaQUAST is also capable of calculating various statistics using raw reads (e.g. database coverage by reads). To use this, you will need use STAR in the pipeline. BUSCO, GeneMarkS-T, and STAR have been installed, and the directories of their exectuables have been added to $PATH. Users do not need to load these modules. The only module required is rnaquast itself.

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 Trinity.fasta idba.fasta \
     --reference Saccharomyces_cerevisiae.R64-1-1.75.dna.toplevel.fa \
     --gtf Saccharomyces_cerevisiae.R64-1-1.75.gtf

rnaQUAST.py -t 12 -o output2 \
     --reference reference.fasta \
     --transcripts transcripts.fasta \
     --left_reads lef.fastq \
     --right_reads right.fastq \
     --busco fungi_odb10