Transabyss
Introduction
Transabyss
is a tool for De novo assembly of RNAseq data using ABySS.
For more information, please check its website: https://bioconda.github.io/recipes/transabyss and its home page on Github.
Versions
2.0.1
Commands
transabyss
transabyss-merge
Module
You can load the modules by:
module load biocontainers
module load transabyss
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 Transabyss on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 12
#SBATCH --job-name=transabyss
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers transabyss
transabyss --name SRR12095148 \
--pe SRR12095148_1.fastq SRR12095148_2.fastq \
--outdir SRR12095148_assembly --threads 12