transabyss
Link to section 'Introduction' of 'transabyss' Introduction
Transabyss is a tool for De novo assembly of RNAseq data using ABySS.
For more information, please check its home page on Github.
Link to section 'Versions' of 'transabyss' Versions
- 2.0.1
Link to section 'Commands' of 'transabyss' Commands
- transabyss
- transabyss-merge
Link to section 'Module' of 'transabyss' Module
You can load the modules by:
module load biocontainers
module load transabyss
Link to section 'Example job' of 'transabyss' 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 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