Trans-ABySS 1.2.0 (Jan 07, 2011)

Bug fixes and performance improved for chimeric transcript codes; also fixed to handle output from different ABySS versions

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

Available downloads


For all platforms (5.2 MB)

Release Notes

State Final release
License BCCA (academic use)

trans-ABySS v1.2.0 user manual

This release contains major bug fixes for chimeric transcript finder scripts. Also the performance is much improved due to the parallelization when running chimeric transcript support jobs on computer cluster.

The code for filtering ABySS contigs is also fixed (utilities/, which is now able to handle different ABySS versions, ranging from 1.1.2 to 1.2.5 (the current latest ABySS version).

The annotation files for hg18 and mm9 can now be downloaded from trans-ABySS software project overview page.


If you are having problems running the included binaries "utilities/SimpleGraph" and "utilities/MergeContigs", you may need to re-compile them from the source. Because the SimpleGraph.cpp used in trans-ABySS is a modified version from the one provided with ABySS, to compile it, you will need various ABySS libraries as well as the modified SimpleGraph.cpp. For convenience, we provide a package that includes all files necessary for compilation. After downloading and unpacking this package, simply type "configure && make" at its root folder. After compilation, you will find the "SimpleGraph" binary under "SimpleGraph/" folder and "MergeContigs" binary under "MergePaths/" folder. Use them to replace the corresponding binaries in your trans-ABySS folder.

If you are having problems running the included binary "analysis/acf/gapblatterBasic", you may need to recompile it from the source "gapblatterBasic.*.cpp", which is provided in the "analysis/acf/" folder. Just use the following command to compile it:

g++ -Wall -Werror -O3 -o gapblatterBasic_v1.6.1 gapblatterBasic.v1.6.cpp



Change log

analysis/acf/*: major updates to acf related scripts including bug fixes and performance improvements (acf VERSION updated to 16.0).

utilities/ fixed the bug that causes the missing of junction contigs for ABySS version 1.2.3 and later; also added codes to check redundancy after junction-contig extension to remove redundant contigs.

wrappers/*: wrapper scripts updated to accommodate changes in various acf scripts and; also added codes to write the work progress to a "log" file.

configs/projects.cfg: updates that accommodate changes in corresponding scripts.

configs/cluster.cfg: added email section