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1.5.2
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@kmnip kmnip released this 14 Nov 23:32
· 51 commits to master since this release
1.5.2
20da23c

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
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