RT Journal Article
SR Electronic
T1 An evaluation of the accuracy and speed of metagenome analysis tools
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 017830
DO 10.1101/017830
A1 Stinus Lindgreen
A1 Karen L. Adair
A1 Paul P. Gardner
YR 2015
UL http://biorxiv.org/content/early/2015/05/15/017830.abstract
AB 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