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MetaSNV: a tool for metagenomic strain level analysis

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Item Type:Article
Title:MetaSNV: a tool for metagenomic strain level analysis
Creators Name:Costea, P.I. and Munch, R. and Coelho, L.P. and Paoli, L. and Sunagawa, S. and Bork, P.
Abstract:We present metaSNV, a tool for single nucleotide variant (SNV) analysis in metagenomic samples, capable of comparing populations of thousands of bacterial and archaeal species. The tool uses as input nucleotide sequence alignments to reference genomes in standard SAM/BAM format, performs SNV calling for individual samples and across the whole data set, and generates various statistics for individual species including allele frequencies and nucleotide diversity per sample as well as distances and fixation indices across samples. Using published data from 676 metagenomic samples of different sites in the oral cavity, we show that the results of metaSNV are comparable to those of MIDAS, an alternative implementation for metagenomic SNV analysis, while data processing is faster and has a smaller storage footprint. Moreover, we implement a set of distance measures that allow the comparison of genomic variation across metagenomic samples and delineate sample-specific variants to enable the tracking of specific strain populations over time. The implementation of metaSNV is available at: http://metasnv.embl.de/.
Keywords:Algorithms, High-Throughput Nucleotide Sequencing, Metagenomics, Sequence Analysis, DNA, Software
Source:PLoS ONE
ISSN:1932-6203
Publisher:Public Library of Science (U.S.A.)
Volume:12
Number:7
Page Range:e0182392
Date:28 July 2017
Official Publication:https://doi.org/10.1371/journal.pone.0182392
PubMed:View item in PubMed

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