Xander: employing a novel method for efficient gene-targeted metagenomic assembly.

ABSTRACT:

Background

Metagenomics can provide important insight into microbial communities. However, assembling metagenomic datasets has proven to be computationally challenging. Current methods often assemble only fragmented partial genes.

Results

We present a novel method for targeting assembly of specific protein-coding genes. This method combines a de Bruijn graph, as used in standard assembly approaches, and a protein profile hidden Markov model (HMM) for the gene of interest, as used in standard annotation approaches. These are used to create a novel combined weighted assembly graph. Xander performs both assembly and annotation concomitantly using information incorporated in this graph. We demonstrate the utility of this approach by assembling contigs for one phylogenetic marker

SUBMITTER: Wang Q 

PROVIDER: S-EPMC4526283 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature