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An evaluation of the accuracy and speed of metagenome analysis tools

View ORCID ProfileStinus Lindgreen, View ORCID ProfileKaren L. Adair, View ORCID ProfilePaul P. Gardner
doi: https://doi.org/10.1101/017830
Stinus Lindgreen
1Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand
2School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
3Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
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  • For correspondence: stinus@binf.ku.dk
Karen L. Adair
1Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand
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Paul P. Gardner
1Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand
2School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
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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. Data sets and results are freely available from http://www.ucbioinformatics.org/metabenchmark.html

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted May 15, 2015.
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An evaluation of the accuracy and speed of metagenome analysis tools
Stinus Lindgreen, Karen L. Adair, Paul P. Gardner
bioRxiv 017830; doi: https://doi.org/10.1101/017830
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An evaluation of the accuracy and speed of metagenome analysis tools
Stinus Lindgreen, Karen L. Adair, Paul P. Gardner
bioRxiv 017830; doi: https://doi.org/10.1101/017830

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