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

PloS One
John MartinMakedonka Mitreva

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 sequence is 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. All aligners report nearly complete genome coverage (>97%) for strains with over 6X depth of coverage, however they differ in speed, memory requirement and ease of use issues such as database size limitations and supported mapping strategies. The selected aligner was tested across a range of parameters to maximize sensitivity while maintaining a low false positive rate. We found that constraining alignment length had more impact on sensitivity than does constraining similarity in all cases tested. However, when reference species were replaced with phylogenet...Continue Reading

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Related Concepts

Escherichia
Body Regions
Neisseria meningitidis
Pseudomonas aeruginosa (antigen)
Genome
Deinococcus
Helicobacter pylori
Unspecified Staphylococcus Infection in Conditions Classified Elsewhere and of Unspecified Site
Escherichia coli K12
Streptococcus

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