MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads.

ABSTRACT: An important step in 'metagenomics' analysis is the assembly of multiple genomes from mixed sequence reads of multiple species in a microbial community. Most conventional pipelines use a single-genome assembler with carefully optimized parameters. A limitation of a single-genome assembler for de novo metagenome assembly is that sequences of highly abundant species are likely misidentified as repeats in a single genome, resulting in a number of small fragmented scaffolds. We extended a single-genome assembler for short reads, known as 'Velvet', to metagenome assembly, which we called 'MetaVelvet', for mixed short reads of multiple species. Our fundamental concept was to first decompose a de Bruijn graph constructed from mixed short reads into individual sub-graphs, and second, to build scaf

SUBMITTER: Namiki T 

PROVIDER: S-EPMC3488206 | biostudies-literature | 2012 Nov

REPOSITORIES: biostudies-literature