Indexed variation graphs for efficient and accurate resistome profiling.

ABSTRACT:

Motivation

Antimicrobial resistance (AMR) remains a major threat to global health. Profiling the collective AMR genes within a metagenome (the 'resistome') facilitates greater understanding of AMR gene diversity and dynamics. In turn, this can allow for gene surveillance, individualized treatment of bacterial infections and more sustainable use of antimicrobials. However, resistome profiling can be complicated by high similarity between reference genes, as well as the sheer volume of sequencing data and the complexity of analysis workflows. We have developed an efficient and accurate method for resistome profiling that addresses these complications and improves upon currently available tools.

Results

Our method combines a variation graph representation of gene sets with a lo

SUBMITTER: Rowe WPM 

PROVIDER: S-EPMC6198860 | biostudies-literature | 2018 Nov

REPOSITORIES: biostudies-literature