Pseudoalignment for metagenomic read assignment

2015/10/26 by Schaeffer, Lorian, Pimentel, Harold, Bray, Nicolas +2 · 2 citations
#FOS: Biological sciences #Genomics (q-bio.GN) #Quantitative Methods (q-bio.QM)

paper · doi:10.48550/arxiv.1510.07371

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.

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• MADRe: Strain-level metagenomic classification through assembly-driven database reduction
• Scaling laws of bacterial and archaeal plasmids

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