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• Genome assembly and analyses pipeline has been retracted.
• Support for SGE qmake has been retracted.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.