Joining Illumina paired-end reads for classifying phylogenetic marker sequences.

ABSTRACT:

Background

Illumina sequencing of a marker gene is popular in metagenomic studies. However, Illumina paired-end (PE) reads sometimes cannot be merged into single reads for subsequent analysis. When mergeable PE reads are limited, one can simply use only first reads for taxonomy annotation, but that wastes information in the second reads. Presumably, including second reads should improve taxonomy annotation. However, a rigorous investigation of how best to do this and how much can be gained has not been reported.

Results

We evaluated two methods of joining as opposed to merging PE reads into single reads for taxonomy annotation using simulated data with sequencing errors. Our rigorous evaluation involved several top classifiers (RDP classifier, SINTAX, and two alignment-based

SUBMITTER: Liu T 

PROVIDER: S-EPMC7071698 | biostudies-literature | 2020 Mar

REPOSITORIES: biostudies-literature