Trans-ABySS 1.4.8 (Sep 13, 2013)

Identifies ITD, PTD, and read-throughs, uses qmake for running pipeline in SGE, and more.

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

Available downloads

Release Notes

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

Trans-ABySS v1.4.8 user manual

Note: the release made on 2013-09-13 was missing the output files of the sample data. Please download the updated archive above (build 20130916) to obtain them.

This is the first public release that identifies partial tandem duplication(PTD), internal tandem duplication(ITD), and read-through events. In fusion analysis, it employs an extra BLAT-alignment step to improve specificity. It also reports additional fields such as breakpoint probe sequence, cytogenetic location, 5' and 3' genes, in/out-of-frame information relevant to gene fusions. To further streamline pipeline execution, it uses qmake in the Sun Grid Engine(SGE) cluster environment.

Change log

Major changes since version 1.4.4 (not in chronological order):

  • ABySS 1.3.5 or above is required to run Trans-ABySS 1.4.8. However, assemblies generated with older 1.3.x versions of ABySS are still supported.
  • The entire pipeline can be run with `qmake' on a SGE cluster.
  • Command variables are wrapped with ${ } in configs/transcriptome.cfg and configs/genome.cfg
  • A new step in the pipeline, 'prepare_contigs', is introduced to balance the size of FASTA files before alignment against the reference genome.
  • Changes in FEM:
    • Overlapping contigs are merged with `abyss-overlap' from ABySS 1.3.5+.
    • Contig IDs use a different notation.
  • Changes in R2C:
    • BWA MEM is the default aligner in both transcriptome and genome pipelines.
  • Changes in C2G:
    • BWA MEM is the default aligner in the genome pipeline.
    • GMAP indexes are expected to be in the same directory as the path of the reference genome defined in configs/transcriptome.cfg and configs/genome.cfg. The name of the GMAP indexes must be same as the name of the reference genome defined in configs/transcriptome.cfg and configs/genome.cfg.
  • Changes in FUSIONS:
    • New event types 'PTD' and 'ITD' are reported in the transcriptome pipeline.
    • Probe sequence at the breakpoint are reported.
    • 'fusions_filtered.tsv' has been splited into 'sense_fusion.tsv', 'antisense_fusion.tsv', 'ITD.tsv', 'PTD.tsv', and 'LSR.tsv',
    • Fusion candidate sequences are aligned with BLAT to confirm the specificity of GMAP's mapping.
    • Cytogenetic location, 5' and 3' genes, in/out-frame information are reported if available in the transcriptome pipeline.
  • Changes in SPLICING:
    • A new event type 'read-through' is reported.