Journal
BMC GENOMICS
Volume 11, Issue -, Pages -Publisher
BMC
DOI: 10.1186/1471-2164-11-461
Keywords
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Funding
- Swiss National Science Foundation
- University of Zurich
- German Science Foundation (DFG)
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Background: Shotgun sequencing of environmental DNA is an essential technique for characterizing uncultivated microbes in situ. However, the taxonomic and functional assignment of the obtained sequence fragments remains a pressing problem. Results: Existing algorithms are largely optimized for speed and coverage; in contrast, we present here a software framework that focuses on a restricted set of informative gene families, using Maximum Likelihood to assign these with the best possible accuracy. This framework ('MLTreeMap'; http://mltreemap.org/) uses raw nucleotide sequences as input, and includes hand-curated, extensible reference information. Conclusions: We discuss how we validated our pipeline using complete genomes as well as simulated and actual environmental sequences.
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