Using pseudoalignment and base quality to accurately quantify microbial community composition.

ABSTRACT: Pooled DNA from multiple unknown organisms arises in a variety of contexts, for example microbial samples from ecological or human health research. Determining the composition of pooled samples can be difficult, especially at the scale of modern sequencing data and reference databases. Here we propose a novel method for taxonomic profiling in pooled DNA that combines the speed and low-memory requirements of k-mer based pseudoalignment with a likelihood framework that uses base quality information to better resolve multiply mapped reads. We apply the method to the problem of classifying 16S rRNA reads using a reference database of known organisms, a common challenge in microbiome research. Using simulations, we show the method is accurate across a variety of read lengths, with different len

SUBMITTER: Reppell M 

PROVIDER: S-EPMC5945057 | biostudies-literature | 2018 Apr

REPOSITORIES: biostudies-literature