  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.
