bcgsc/transabyss

de novo assembly of RNA-seq data using ABySS

Trans-ABySS

De novo assembly of RNAseq data using ABySS

Ka Ming Nip and Readman Chiu

Copyright 2018 Canada's Michael Smith Genome Sciences Centre, BC Cancer

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)

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Program requirements for transabyss and transabyss-merge:

• ABySS 2.0.x
• Python 2.7.x or Python 3.6.x
• python-igraph 0.7.x
• BLAT

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

pip install igraph

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

To test transabyss on our sample dataset:

bash sample_dataset/assemble.sh

Please check out our short tutorial for more information on the usage of each application.

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