Skip to content
This repository was archived by the owner on Jun 18, 2026. It is now read-only.

Home

Jump to bottom
asmariyaz23 edited this page Jul 18, 2018 · 3 revisions

Cancer Transcriptome Analysis Toolkit Metagenomics

The Trinity Cancer Transcriptome Analysis Toolkit (CTAT) aims to provide tools for leveraging RNA-Seq to gain insights into the biology of cancer transcriptomes.

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.

3 ways to get started:

  1. git clone https://github.com/NCIP/ctat-metagenomics.git
  2. Conda installation
  3. Galaxy toolshed installation of the tool
  4. Run this tool via our Trinity CTAT Galaxy Portal.

User support

Contact us on our google group https://groups.google.com/forum/#!forum/trinity_ctat_users

Kim, D., Song, L., Breitwieser, F. P., & Salzberg, S. L. (2016). Centrifuge: rapid and sensitive classification of metagenomic sequences. Genome Research, 26(12), 1721–1729. https://doi.org/10.1101/gr.210641.116

Clone this wiki locally