1.5.2
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
make
cd ..
export PATH=$PWD/prereqs/bin:$PATH
export LD_LIBRARY_PATH=$PWD/prereqs/lib
transabyss:
- 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 specifing zero iterations:
--gsim 0
- Option to skip the redundancy removal procedure:
--noblat
transabyss-merge:
- 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.
transabyss-analyze:
- Fixed bug where cluster jobs would result in a non-zero exit status.
- Changed the analyses output directory names:
fusion
,indel
,splice