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      COVER: a priori estimation of coverage for metagenomic sequencing.

      1 , ,

      Environmental microbiology reports

      Wiley

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          Abstract

          In any metagenomic project, the coverage obtained for each particular species depends on its abundance. This makes it difficult to determine a priori the amount of DNA sequencing necessary to obtain a high coverage for the dominant genomes in an environment. To aid the design of metagenomic sequencing projects, we have developed COVER, a web-based tool that allows the estimation of the coverage achieved for each species in an environmental sample. COVER uses a set of 16S rRNA sequences to produce an estimate of the number of operational taxonomic units (OTUs) in the sample, provides a taxonomic assignment for them, estimates their genome sizes and, most critically, corrects for the number of unobserved OTUs. COVER then calculates the amount of sequencing needed to achieve a given goal. Our tests and simulations indicate that the results obtained through COVER are in very good agreement with the experimental results.

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          Author and article information

          Journal
          Environ Microbiol Rep
          Environmental microbiology reports
          Wiley
          1758-2229
          1758-2229
          Jun 2012
          : 4
          : 3
          Affiliations
          [1 ] Systems Biology Programme, Centro Nacional de Biotecnología (CNB-CSIC). C/Darwin 3, 28049 Madrid, Spain.
          Article
          10.1111/j.1758-2229.2012.00338.x
          23760797

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