Trans-ABySS 1.4.4 (Oct 09, 2012)

Supports both transcriptome and genome assemblies. A more robust pipeline and improvement to the 3 analysis suites (fusions, indels, and splicing).

For additional information about this project, please visit the overview page .

Available downloads

Trans-ABySS 1.4.4

For Linux (2.1 MB)

Release Notes

State Final release
License BCCA (academic use)
Release Manager Readman Chiu

trans-ABySS v1.4.4 user manual

This new release supports analysis of both transcriptome and genome assemblies. It recommends using GMAP for alignment of transcriptome contigs and BWA-SW for genome contigs to the reference genome, and supports SAM alignment output format in addition to PSL. The wrapper for running the pipeline is more robust and there are significant upgrades to the analysis suites (fusions, indels, and splicing).

Change log

# new '' wrapper to run both transcriptome and genome pipeline
# uses GMAP for aligning transcriptome contigs
# uses BWA-SW for aligning transcriptome contigs
# project specific run paramters can be specified in .cfg files
# '' and '' for handling reads-to-contigs alignment
# latest version of Pysam (0.6) used
# bugfix in fusion code: deletion breakpoint now reported correctly
# reciprocal fusion events now reported
# 'orientations' and 'descriptor' fields added to fusion output
# indel code uses '.tsv' file extension instead of '.txt'
# supports the GAF annotation format that is adopted by TCGA
# overlap events with DGV entries
# handling of differences in chromosome names between FASTA file and annotation files
# stop outputting evidence reads for splicing code

# wrapper can re-run alignment and analysis
# '' now can run abyss-map and remove intermediate files
# bug in labeling deletions in fusions output fixed
# overlaps deletions in fusions output with dbSNP

# bug fixed in wrapper for handling project-specific parameters
# overlaps deletions in fusions output with DGV

# handling trand-specific transcriptome
# input file (for wrapper) format change
# will order GMAP output the same as the input
# Get rid of sequence in .sam files before output
# upgraded for splicing
# sam to psl converter - generate track (compressed)
# won't use chastity-failed reads in SNV confirmation

# all chromosome names will be the same as in the FASTA file
# same transcript will be used in indel code so that ORF effect can be reported
# bugs in '' fixed
# impose maximum size of deletion in fusion output to be overlapped with dbSNP: 1Mb
# bugfix in fusion code: deletion descriptor now reported correctly
# extra information reported by fusion code: transcripts, senses, exons/introns, exon_bounds, 5' gene, 3' gene, 5' exon, 3' exon, frame
# require contigs FASTA file to be given for fusion run