GraftM: a tool for scalable, phylogenetically informed classification of genes within metagenomes.

ABSTRACT: Large-scale metagenomic datasets enable the recovery of hundreds of population genomes from environmental samples. However, these genomes do not typically represent the full diversity of complex microbial communities. Gene-centric approaches can be used to gain a comprehensive view of diversity by examining each read independently, but traditional pairwise comparison approaches typically over-classify taxonomy and scale poorly with increasing metagenome and database sizes. Here we introduce GraftM, a tool that uses gene specific packages to rapidly identify gene families in metagenomic data using hidden Markov models (HMMs) or DIAMOND databases, and classifies these sequences using placement into pre-constructed gene trees. The speed and accuracy of GraftM was benchmarked with in silico an

SUBMITTER: Boyd JA 

PROVIDER: S-EPMC6007438 | biostudies-literature | 2018 Jun

REPOSITORIES: biostudies-literature