Trans-ABySS 1.3.2 (Feb 29, 2012)
Compatibility with ABySS 1.3.2; Streamlining of pipeline and configuration files; Analysis code improvement
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 v1.3.2 user manual
(Note: For those downloaded Trans-ABySS v1.3.2 and were missing "cnv.py", please download cnv.py and place it in the "analysis" directory.)
Trans-ABySS v1.3.2 is now compatible with ABySS v1.3.2. A single configuration file has now replaced multiple ones for better clarity. Contig filtering, extension, and merging are now performed using ABySS utilities to improve on performance. The analysis modules have undergone many improvements. The analysis pipeline is using the feature of job-dependency of Sun Grid Engine to reduce the amount of human monitoring.
Change log
Annotation files:
Annotation files are no longer provided in the download package. Users are instead provided a Unix shell script to download files from the UCSC genome browser on common genomes such as hg19, hg18, and mm9. Please refer to the user manual for details.
Pre-analysis:
1. Use abyss-filtergraph and abyss-junction for filtering and extending ABySS contigs
2. Merging of contigs is using abyss-map instead of Blat.
Analysis:
There are many changes in the analysis modules since v1.2.0, here are the main ones:
fusion.py
1. reports breakpoint and type of rearrangement in output file
2. "local" filtering: if regions belong to the same gene or within 5kb of each other
model_matcher.py
1. reports proper exon number
2. corrects Blat alignments around exon junctions where appropriate
snv_caller.py
1. reports inversion events
2. uneven SNV substitution will become deletion and insertion
3. default upper size limit for indel (10kb) removed
