  Metagenomics research has accelerated the studies of microbial organisms,
providing insights into the composition and potential functionality of various
microbial communities. Metatranscriptomics (studies of the transcripts from a
mixture of microbial species) and other meta-omics approaches hold even greater
promise for providing additional insights into functional and regulatory
characteristics of the microbial communities. Current metatranscriptomics
projects are often carried out without matched metagenomic datasets (of the
same microbial communities). For the projects that produce both
metatranscriptomic and metagenomic datasets, their analyses are often not
integrated. Metagenome assemblies are far from perfect, partially explaining
why metagenome assemblies are not used for the analysis of metatranscriptomic
datasets. Here we report a reads mapping algorithm 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 developed an application of this mapping
algorithm: a reference based approach to metatranscriptome assembly using
graphs of metagenome assembly as the reference. Our results show that this new
approach (called TAG) helps to assemble substantially more transcripts that
otherwise would have been missed or truncated because of the fragmented nature
of the reference metagenome. TAG was implemented in C++ and has been tested
extensively on the linux platform. It is available for download as open source
at http://omics.informatics.indiana.edu/TAG.
