- Description: Trans-ABySS (Assembly By Short Sequences) is a software pipeline written in Python and Perl for analyzing ABySS-assembled transcriptome contigs.
- Version: 1.5.4
- Modules: transabyss/1.5.5
- Licence: BCCA (BC Cancer Agency) academic use
This pipeline can be applied to assemblies generated across a wide range of k values. It first reduces the dataset into smaller sets of non-redundant contigs, and identifies splicing events including exon-skipping, novel exons, retained introns, novel introns, and alternative splicing. The Trans-ABySS algorithms are also able to estimate gene expression levels, identify potential polyadenylation sites, as well as candidate gene-fusion events 
Because of the nature of such tasks, it may be more appropriate to use highmem nodes rather than standard compute nodes.
#!/bin/bash #SBATCH -J transabyss #SBATCH -N 1 #SBATCH -n 28 #SBATCH -o %N-%j.log #SBATCH -e %N-%j.err #SBATCH -p compute #SBATCH --exclusive module add transabyss/1.5.5 transabyss --pe R1.fq R2.fq --name transabyss --threads 28 -k 25 --length 200
[username@login01 ~]$ sbatch transabyss.job Submitted batch job 289555