Warning

This repository has been archived and is no longer maintained.
The code is provided for historical reference and may contain unpatched or unknown vulnerabilities.
It should not be used in production systems.

#ctat-metagenomics For foreign transcript detection, we leverage Centrifuge and Kraken, leveraging RNA-Seq reads and Trinity-reconstructed transcripts. Our efforts here are being carried out in collaboration with the group of Steven Salzberg at JHU.

Click the 'wiki' link at top for the ctat-metagenomics documentation.

Note, if you're going to clone the code from github, do it recursively like so:

git clone --recursive https://github.com/NCIP/ctat-metagenomics.git