rnaquast
Link to section 'Introduction' of '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/.
Link to section 'Versions' of 'rnaquast' Versions
- 2.2.1
Link to section 'Commands' of 'rnaquast' Commands
- rnaQUAST.py
Link to section 'Dependencies de novo quality assessment and read alignment' of 'rnaquast' Dependencies de novo quality assessment and read alignment
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 executables have been added to $PATH. Users do not need to load these modules. The only module required is rnaquast itself.
Link to section 'Module' of 'rnaquast' Module
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 executables have been added to $PATH. Users do not need to load these modules. The only module required is rnaquast itself.
You can load the modules by:
module load biocontainers
module load rnaquast
Link to section 'Example job' of 'rnaquast' Example job
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