Pseudoalignment for metagenomic read assignment

Abstract

We explore connections between metagenomic read assignment and the quantification of transcripts from RNA-Seq data. In particular, we show that the recent idea of pseudoalignment introduced in the RNA-Seq context is suitable in the metagenomics setting. When coupled with the Expectation-Maximization (EM) algorithm, reads can be assigned far more accurately and quickly than is currently possible with state of the art software.

Replaced accidentally duplicated figure with correct version; fixed some issues with figure generation and labeling; fixed problem with some missing genomes from database; added link to GitHub repo containing analysis code; included assessment of aggregate sensitivity and precision; clarified assessment metrics used