The Amordad database engine for metagenomics.

ABSTRACT:

Motivation

Several technical challenges in metagenomic data analysis, including assembling metagenomic sequence data or identifying operational taxonomic units, are both significant and well known. These forms of analysis are increasingly cited as conceptually flawed, given the extreme variation within traditionally defined species and rampant horizontal gene transfer. Furthermore, computational requirements of such analysis have hindered content-based organization of metagenomic data at large scale.

Results

In this article, we introduce the Amordad database engine for alignment-free, content-based indexing of metagenomic datasets. Amordad places the metagenome comparison problem in a geometric context, and uses an indexing strategy that combines random hashing with a regula

SUBMITTER: Behnam E 

PROVIDER: S-EPMC4184256 | biostudies-literature | 2014 Oct

REPOSITORIES: biostudies-literature