2.0.1

• Switch license to GPL3 (same as ABySS)
• Support for Python 3; Python 2 is still supported (tested on versions 2.7.14 and 3.6.4)

2.0.0

• Supports ABySS 2.0.x
• No changes to assembly algorithms

1.5.5

transabyss:

• set default shortest contig length to 100 bp, ie. --length 100
• skip blat alignments; can be turned on with --useblat

transabyss-merge:

• no changes

1.5.4

• Removed transabyss-analyze and its associated modules
• We recommend using PAVFinder for structural variant detection.

1.5.3

Bugfixes:

• incompatibility issue with the latest version of BLAT (#3)
• fatal error in abyss-filtergraph

Minor Updates:

• Updated prereq/makefile to install the latest version of required software packages

It is highly recommended to use PAVFinder (in place of transabyss-analyze) for structural variant detection.

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

1.5.1

• Support strand-specific RNAseq data.
• Major improvement in assembly quality; both rare and common transcripts can be
  assembled well with "small" k-mer sizes (ie. 25~32).
• Package has been divided into 3 main applications:
  1. transabyss - RNAseq assembler at a single k-mer size
  2. transabyss-merge - merge multiple assemblies from (i)
  3. transabyss-analyze - analyze an assembly, either from (i) or (ii), for
     structural variants and novel splice variants
• Analysis results are NOT screened against dbSNP, DGV, etc. anymore.
• Genome assembly and analyses pipeline has been retracted.
• Support for SGE qmake has been retracted.

Program requirements for 'transabyss' and 'transabyss-merge':

• ABySS 1.5.1+ https://github.com/bcgsc/abyss/releases
• Python 2.7.6+ https://www.python.org/download/releases/2.7.6/
• python-igraph 0.7.0+ http://igraph.org/python/#downloads
• BLAT http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/blat/blat

Program requirements for 'transabyss-analyze':

• Python 2.7.6+ https://www.python.org/download/releases/2.7.6/
• BLAT http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/blat/blat
• Pysam http://code.google.com/p/pysam/
• BioPython http://biopython.org/wiki/Download
• Bowtie2 http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
• GMAP/GSNAP http://research-pub.gene.com/gmap/
• Samtools http://sourceforge.net/projects/samtools/files/samtools/
• reference genome and annotations for the organism of interest

Required Python packages (python-igraph, Pysam, BioPython) can be installed
easily with pip, ie.

pip install python-igraph
pip install pysam
pip install biopython

Other required softwares must be accessible from your PATH environment variable.

To test `transabyss' on our sample dataset:

bash sample_dataset/assemble.sh

To test `transabyss-analyze' on our sample dataset:

bash sample_dataset/analyze.sh

Please see TUTORIAL.txt for more information on the usage of each application.