A comparative study of metagenomics analysis pipelines at the species level

9 Many metagenomics classification tools have been developed with the rapid growth of the 10 metagenomics field. However, the classification of closely related species remains a challenge for 11 this field. Here, we compared MetaPhlAn2, kallisto and Kraken for their performances in two 12 metagenomics settings, human metagenomics and environmental metagenomics. Our comparative 13 study showed that kallisto demonstrated higher sensitivity than MetaPhlAn2 and Kraken and better 14 quantification accuracy than Kraken at the species level. We also showed that classification tools 15 that run on full reference genomes misidentified many species that were not truly present. In order 16 to reduce false positives, we introduced marker genes from MetaPhlAn2 into our pipeline, which 17 uses kallisto for the classification step, as an additional filtering step for species detection. 18 19 Introduction 20 The advent of shotgun metagenomic sequencing greatly facilitated the identification and 21 classification of microbes by providing a means to detect phenotypically aberrant or unculturable 22 microbes [1]. It allows a much faster and cheaper taxonomic profiling of microbial communities 23 in different ecosystems such as the microbiome in human, soil and ocean. With the rising use of 24 . CC-BY-NC-ND 4.0 International license peer-reviewed) is the author/funder. It is made available under a The copyright holder for this preprint (which was not . http://dx.doi.org/10.1101/081141 doi: bioRxiv preprint first posted online Oct. 15, 2016;