Optimizing read mapping to reference genomes to determine composition and species prevalence in microbial communities.

Martin, John and Sykes, Sean and Young, Sarah and Kota, Karthik and Sanka, Ravi and Sheth, Nihar and Orvis, Joshua and Sodergren, Erica and Weinstock, George M and Mitreva, Makedonka and Wang, Zhengyuan (2012) Optimizing read mapping to reference genomes to determine composition and species prevalence in microbial communities. PLoS One, 7 (6). e36427.

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Abstract

The Human Microbiome Project (HMP) aims to characterize the microbial communities of 18 body sites from healthy individuals. To accomplish this, the HMP generated two types of shotgun data: reference shotgun sequences isolated from different anatomical sites on the human body and shotgun metagenomic sequences from the microbial communities of each site. The alignment strategy for characterizing these metagenomic communities using available reference sequenceis important to the success of HMP data analysis. Six next - generation aligners were used to align a community of known composition against a database comprising reference organisms known to be present in that community.

Item Type: Article
Subjects: Medical and Health Sciences > Basic medicine
Divisions: Faculty of Medical Science
Depositing User: Mirjana Kocaleva
Date Deposited: 03 Dec 2012 11:48
Last Modified: 03 Dec 2012 11:48
URI: http://eprints.ugd.edu.mk/id/eprint/2882

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