MetaBEETL: high-throughput analysis of heterogeneous microbial populations from shotgun DNA sequences.

ABSTRACT: Environmental shotgun sequencing (ESS) has potential to give greater insight into microbial communities than targeted sequencing of 16S regions, but requires much higher sequence coverage. The advent of next-generation sequencing has made it feasible for the Human Microbiome Project and other initiatives to generate ESS data on a large scale, but computationally efficient methods for analysing such data sets are needed.Here we present metaBEETL, a fast taxonomic classifier for environmental shotgun sequences. It uses a Burrows-Wheeler Transform (BWT) index of the sequencing reads and an indexed database of microbial reference sequences. Unlike other BWT-based tools, our method has no upper limit on the number or the total size of the reference sequences in its database. By capturing sequen

SUBMITTER: Ander C 

PROVIDER: S-EPMC3622627 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature