Estimating DNA coverage and abundance in metagenomes using a gamma approximation.

ABSTRACT:

Motivation

Shotgun sequencing generates large numbers of short DNA reads from either an isolated organism or, in the case of metagenomics projects, from the aggregate genome of a microbial community. These reads are then assembled based on overlapping sequences into larger, contiguous sequences (contigs). The feasibility of assembly and the coverage achieved (reads per nucleotide or distinct sequence of nucleotides) depend on several factors: the number of reads sequenced, the read length and the relative abundances of their source genomes in the microbial community. A low coverage suggests that most of the genomic DNA in the sample has not been sequenced, but it is often difficult to estimate either the extent of the uncaptured diversity or the amount of additional sequencing that

SUBMITTER: Hooper SD 

PROVIDER: S-EPMC2815663 | biostudies-literature | 2010 Feb

REPOSITORIES: biostudies-literature