Estimating the total genome length of a metagenomic sample using k-mers.

ABSTRACT:

Background

Metagenomic sequencing is a powerful technology for studying the mixture of microbes or the microbiomes on human and in the environment. One basic task of analyzing metagenomic data is to identify the component genomes in the community. This task is challenging due to the complexity of microbiome composition, limited availability of known reference genomes, and usually insufficient sequencing coverage.

Results

As an initial step toward understanding the complete composition of a metagenomic sample, we studied the problem of estimating the total length of all distinct component genomes in a metagenomic sample. We showed that this problem can be solved by estimating the total number of distinct k-mers in all the metagenomic sequencing data. We proposed a method for

SUBMITTER: Hua K 

PROVIDER: S-EPMC6456951 | biostudies-literature | 2019 Apr

REPOSITORIES: biostudies-literature