Trans-ABySS 1.5.2 (Nov 14, 2014)

Simplify the installation of required softwares. Less temporary disk space usage in assembly. New options, bugfixes, and improvements.

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

Available downloads

Release Notes

State Final release
License BCCA (academic use)
Release Manager Ka Ming Nip

General Updates:
* A makefile to simplify the process of downloading and installing the required softwares (except for ABySS) under the Trans-ABySS `prereqs` directory. Please note the specified versions of the softwares in the makefile. The makefile probably does not work on all platforms; please modify the makefile as you like. Here is an example usage of this makefile:
cd prereqs
cd ..
export PATH=$PWD/prereqs/bin:$PATH
export LD_LIBRARY_PATH=$PWD/prereqs/lib

* Incorporate ABySS distance estimates for path extensions.
* Lowered the amount of diskspace required for temporary files.
* Skip paired end assembly when the de Bruijn graph assembly generates an edgeless adjacency graph.
* Option to skip graph simplification by specifying zero iterations: `--gsim 0`
* Option to skip the redundancy removal procedure: `--noblat`

* 2 new options to merge assemblies with abyss-map: `--abyssmap`, `--abyssmap-itr`. These two abyss-map methods are quicker than the default BLAT method, but they require more memory and cannot merge contigs with mismatches. `--abyssmap` and `--abyssmap-itr` should generate the same merged assembly. `--abyssmap-itr` requires less memory but it is slower.

* Fixed bug where cluster jobs would result in a non-zero exit status.
* Changed the analyses output directory names: `fusion`, `indel`, `splice`