https://github.com/bcgsc/transabyss

de novo assembly of RNA-seq data using ABySS
https://github.com/bcgsc/transabyss

bioinformatics rna-seq transcriptome transcriptome-assembly

Last synced: 15 days ago
JSON representation

de novo assembly of RNA-seq data using ABySS

• Host: GitHub
• URL: https://github.com/bcgsc/transabyss
• Owner: bcgsc
• License: other
• Created: 2014-07-08T17:42:46.000Z (almost 11 years ago)
• Default Branch: master
• Last Pushed: 2023-07-21T02:39:34.000Z (almost 2 years ago)
• Last Synced: 2025-04-19T19:34:38.894Z (about 1 month ago)
• Topics: bioinformatics, rna-seq, transcriptome, transcriptome-assembly
• Language: Python
• Homepage:
• Size: 724 KB
• Stars: 34
• Watchers: 19
• Forks: 14
• Open Issues: 4
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

Awesome Lists containing this project

README

        
[![Release](https://img.shields.io/github/release/bcgsc/transabyss.svg)](https://github.com/bcgsc/transabyss/releases)

[![Downloads](https://img.shields.io/github/downloads/bcgsc/transabyss/total?logo=github)](https://github.com/bcgsc/transabyss/releases/download/2.0.1/transabyss-2.0.1.zip)

[![Conda](https://img.shields.io/conda/dn/bioconda/transabyss?label=Conda)](https://anaconda.org/bioconda/transabyss)

[![Issues](https://img.shields.io/github/issues/bcgsc/transabyss.svg)](https://github.com/bcgsc/transabyss/issues)

# Trans-ABySS

## *De novo* assembly of RNAseq data using ABySS

[Ka Ming Nip](mailto:[email protected]) and [Readman Chiu](mailto:[email protected])

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

Please use our [Google Group](mailto:[email protected]) for [discussions and

support](https://groups.google.com/d/forum/trans-abyss).

  

You may also create [issues](https://github.com/bcgsc/transabyss/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)](http://www.nature.com/nmeth/journal/v7/n11/full/nmeth.1517.html)

--------------------------------------------------------------------------------

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

  * [ABySS 2.0.x](https://github.com/bcgsc/abyss/releases)

  * [Python 2.7.x](https://www.python.org/download/releases/2.7.14/) or [Python 3.6.x](https://www.python.org/download/releases/3.6.4/)

  * [python-igraph 0.7.x](http://igraph.org/python/#downloads)

  * [BLAT](http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/blat/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](TUTORIAL.md) for more information on the usage of each application.

--------------------------------------------------------------------------------

EOF