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Metagenomics research has accelerated the studies of microbial organisms,providing insights into the composition and potential functionality of variousmicrobial communities. Metatranscriptomics (studies of the transcripts from amixture of microbial species) and other meta-omics approaches hold even greaterpromise for providing additional insights into functional and regulatorycharacteristics of the microbial communities. Current metatranscriptomicsprojects are often carried out without matched metagenomic datasets (of thesame microbial communities). For the projects that produce bothmetatranscriptomic and metagenomic datasets, their analyses are often notintegrated. Metagenome assemblies are far from perfect, partially explainingwhy metagenome assemblies are not used for the analysis of metatranscriptomicdatasets. Here we report a reads mapping algorithm for mapping of short readsonto a de Bruijn graph of assemblies. A hash table of junction k-mers (k-mersspanning branching structures in the de Bruijn graph) is used to facilitatefast mapping of reads to the graph. We developed an application of this mappingalgorithm: a reference based approach to metatranscriptome assembly usinggraphs of metagenome assembly as the reference. Our results show that this newapproach (called TAG) helps to assemble substantially more transcripts thatotherwise would have been missed or truncated because of the fragmented natureof the reference metagenome. TAG was implemented in C++ and has been testedextensively on the linux platform. It is available for download as open sourceat http://omics.informatics.indiana.edu/TAG.

Utilizing de Bruijn graph of metagenome assembly for metatranscriptome analysis