Trans-ABySS 1.1.0 (Nov 22, 2010)
Added new code for finding putative chimeric transcripts, and adjusted stage 1 filtering to reduce the number of small contigs.
For additional information about this project, please visit the overview page .
Available downloads
Release Notes
| State | Final release |
|---|---|
| License | BCCA (academic use) |
This release extends Trans-ABySS’ functionality for finding putative chimeric transcripts that may involve one or more genes. Such transcripts can result from gene fusions, but can also reflect a wide range of genome rearrangements (e.g. inversions or duplications), or, potentially, trans-splicing events. Resolving whether such contigs represent genomic rearrangements or trans-splicing would require genome data. Across the range of types of chimeric transcripts, only some types are direct representations of the in vivo transcripts that were the source of the short reads that were assembled into the contigs. Other types require more experience to interpret.
In the previous version (v1.0.1) we adjusted filtering to retain certain contigs that had been filtered out in v1.0. However, this generated a large number of small contigs (length between k and 2k-2) that were not aligned/reported properly by BLAT in fastmap mode. In v1.1.0, we have addressed this. We first extend junction contigs by merging with all graph ancestors/successors that are linked by unambiguous edges, then we remove all contigs that are not longer than the read length. Compared with the previous version (v1.0.1), v1.1.0's filtering reduces the number of contigs by a factor of 2~6 for the normal and tumor libraries that we have assessed.
Change log
Annotation files are separated from source codes. Scripts are added to automatically download and set up annotation folders for hg18 and mm9 if required.
assembly.py: update junction contig extensions (use SimpleGraph and MergeContigs), add read length filtering
reads_to_contigs.py: bug fix
fachain: add colorspace support
wrappers/run_acf.pl, wrappers/acfinder.pl, analysis/acf/*: new codes for finding putative chimeric transcript events
