An evaluation of the accuracy and speed of metagenome analysis tools View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2016-05

AUTHORS

Stinus Lindgreen, Karen L. Adair, Paul P. Gardner

ABSTRACT

Metagenome studies are becoming increasingly widespread, yielding important insights into microbial communities covering diverse environments from terrestrial and aquatic ecosystems to human skin and gut. With the advent of high-throughput sequencing platforms, the use of large scale shotgun sequencing approaches is now commonplace. However, a thorough independent benchmark comparing state-of-the-art metagenome analysis tools is lacking. Here, we present a benchmark where the most widely used tools are tested on complex, realistic data sets. Our results clearly show that the most widely used tools are not necessarily the most accurate, that the most accurate tool is not necessarily the most time consuming, and that there is a high degree of variability between available tools. These findings are important as the conclusions of any metagenomics study are affected by errors in the predicted community composition and functional capacity. Data sets and results are freely available from http://www.ucbioinformatics.org/metabenchmark.html. More... »

PAGES

19233

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  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1038/srep19233

    DOI

    http://dx.doi.org/10.1038/srep19233

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1051309616

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/26778510


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