Genometa--a fast and accurate classifier for short metagenomic shotgun reads.

ABSTRACT:

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Metagenomic studies use high-throughput sequence data to investigate microbial communities in situ. However, considerable challenges remain in the analysis of these data, particularly with regard to speed and reliable analysis of microbial species as opposed to higher level taxa such as phyla. We here present Genometa, a computationally undemanding graphical user interface program that enables identification of bacterial species and gene content from datasets generated by inexpensive high-throughput short read sequencing technologies. Our approach was first verified on two simulated metagenomic short read datasets, detecting 100% and 94% of the bacterial species included with few false positives or false negatives. Subsequent comparative benchmarking analysis against thr

SUBMITTER: Davenport CF 

PROVIDER: S-EPMC3424124 | biostudies-literature | 2012

REPOSITORIES: biostudies-literature