Applications/transabyss

Application Details

• 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

Usage

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 [1]

Because of the nature of such tasks, it may be more appropriate to use highmem nodes rather than standard compute nodes.

Batch Submission

#!/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

Further Information

• http://www.bcgsc.ca/platform/bioinfo/software/trans-abyss
• http://hpc.mediawiki.hull.ac.uk/Applications/ABySS
• https://en.wikipedia.org/wiki/De_novo_transcriptome_assembly#Trans-ABySS

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