Introduction

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/.

Publications

  1. metaSNV: A tool for metagenomic strain level analysis.
    Cite this
    Costea PI, Munch R, Coelho LP, Paoli L, Sunagawa S, Bork P, 2017-01-01 - PloS one

Credits

  1. Paul Igor Costea
    Developer

    Structural and Computational Biology Unit, European Molecular Biology Laboratory, Germany

  2. Robin Munch
    Developer

    Structural and Computational Biology Unit, European Molecular Biology Laboratory, Germany

  3. Luis Pedro Coelho
    Developer

    Structural and Computational Biology Unit, European Molecular Biology Laboratory, Germany

  4. Lucas Paoli
    Developer

    Department of Biology, Ecole normale supérieure, France

  5. Shinichi Sunagawa
    Developer

    Department of Biology, Institute of Microbiology, Switzerland

  6. Peer Bork
    Investigator

    Molecular Medicine Partnership Unit, Heidelberg, Germany

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Summary
AccessionBT001459
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesC++
User InterfaceTerminal Command Line
Download Count0
Country/RegionGermany
Submitted ByPeer Bork