ctat_metagenomics is a component of the Trinity Cancer Transcriptome Analysis Toolkit (CTAT). CTAT's metagenomics is a classifier for metagenomic sequences (RNA-Seq) for foreign transcript detection. It leverages Centrifuge, a novel microbial classification engine that enables rapid, accurate, and sensitive labeling of reads and quantification of species, and Kraken. As well, we are 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.

For more information:

https://ccb.jhu.edu/software/centrifuge/manual.shtml#what-is-centrifuge