Bambus 2: scaffolding metagenomes.

ABSTRACT:

Motivation

Sequencing projects increasingly target samples from non-clonal sources. In particular, metagenomics has enabled scientists to begin to characterize the structure of microbial communities. The software tools developed for assembling and analyzing sequencing data for clonal organisms are, however, unable to adequately process data derived from non-clonal sources.

Results

We present a new scaffolder, Bambus 2, to address some of the challenges encountered when analyzing metagenomes. Our approach relies on a combination of a novel method for detecting genomic repeats and algorithms that analyze assembly graphs to identify biologically meaningful genomic variants. We compare our software to current assemblers using simulated and real data. We demonstrate that the repe

SUBMITTER: Koren S 

PROVIDER: S-EPMC3198580 | biostudies-literature | 2011 Nov

REPOSITORIES: biostudies-literature