Ka Ming Nip, Readman Chiu

Copyright 2015 Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency

Please use our Google Group for discussions and support.

You may also create issues on our GitHub repository.

If you use Trans-ABySS, please cite:

Robertson, G., et al. 2010. De novo assembly and analysis of RNA-seq data. Nature Methods 7, 909-912(2010)

Program requirements for transabyss and transabyss-merge:

• ABySS 1.5.2
• Python 2.7.6+
• python-igraph 0.7.0+
• BLAT

Program requirements for transabyss-analyze:

• Python 2.7.6+
• BLAT
• Pysam
• BioPython
• Bowtie2
• GMAP/GSNAP
• Samtools
• reference genome and annotations for the organism of interest

Required Python packages (ie. 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 usage of each application.

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