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:
- transabyss - RNAseq assembler at a single k-mer size
- transabyss-merge - merge multiple assemblies from (i)
- 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- Genome assembly and analyses pipeline has been retracted.
- Support for SGE qmake has been retracted.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.