TAG

TAG is a tool for metatranscriptome assembly using de Bruijn graph of matched metagenome as the reference.

TAG is an application of a reads mapping algorithm that we developed for mapping of short reads onto a de Bruijn graph of assemblies. A hash table of junction k-mers (k-mers spanning branching structures in the de Bruijn graph) is used to facilitate fast mapping of reads to the graph.

We have shown that TAG helps to assemble substantially more transcripts from metatranscriptomic datasets that otherwise would have been missed or truncated because of the fragmented nature of the reference metagenome.

Toy datasets for testing TAG (big file!) can be downloaded from http://omics.informatics.indiana.edu/TAG/.

Reference: Yuzhen Ye and Haixu Tang. Utilizing de Bruijn graph of metagenome assembly for metatranscriptome analysis. Bioinformatics (2015)
doi: 10.1093/bioinformatics/btv510.