Journal article

Correcting index databases improves metagenomic studies

Guillaume Méric, Ryan Wick, Stephen Watts, Kathryn Holt, Michael Inouye

Published : 2019

Abstract

Abstract Assessing the taxonomic composition of metagenomic samples is an important first step in understanding the biology and ecology of microbial communities in complex environments. Despite a wealth of algorithms and tools for metagenomic classification, relatively little effort has been put into the critical task of improving the quality of reference indices to which metagenomic reads are assigned. Here, we inferred the taxonomic composition of 404 publicly available metagenomes from human, marine and soil environments, using custom index databases modified according to two factors: the number of reference genomes used to build the databases, and the monophyletic strictness of species d..

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