Unsupervised binning of environmental genomic fragments based on an error robust selection of l-mers.

ABSTRACT:

Background

With the rapid development of genome sequencing techniques, traditional research methods based on the isolation and cultivation of microorganisms are being gradually replaced by metagenomics, which is also known as environmental genomics. The first step, which is still a major bottleneck, of metagenomics is the taxonomic characterization of DNA fragments (reads) resulting from sequencing a sample of mixed species. This step is usually referred as "binning". Existing binning methods are based on supervised or semi-supervised approaches which rely heavily on reference genomes of known microorganisms and phylogenetic marker genes. Due to the limited availability of reference genomes and the bias and instability of marker genes, existing binning methods may not be applicable

SUBMITTER: Yang B 

PROVIDER: S-EPMC3165929 | biostudies-literature | 2010 Apr

REPOSITORIES: biostudies-literature