abstract
motivation: 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.
results: 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.
availability: 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.
contact: yye@indiana.edu.