A Filtering Method to Generate High Quality Short Reads Using Illumina Paired-End Technology Journal Article


Authors: Eren, A. Murat; Vineis, Joseph H.; Morrison, Hilary G.; Sogin, Mitchell L.
Article Title: A Filtering Method to Generate High Quality Short Reads Using Illumina Paired-End Technology
Abstract: Consensus between independent reads improves the accuracy of genome and transcriptome analyses, however lack of consensus between very similar sequences in metagenomic studies can and often does represent natural variation of biological significance. The common use of machine-assigned quality scores on next generation platforms does not necessarily correlate with accuracy. Here, we describe using the overlap of paired-end, short sequence reads to identify error-prone reads in marker gene analyses and their contribution to spurious OTUs following clustering analysis using QIIME. Our approach can also reduce error in shotgun sequencing data generated from libraries with small, tightly constrained insert sizes. The open-source implementation of this algorithm in Python programming language with user instructions can be obtained from https://github.com/meren/illumina-utils.
Keywords: SEQUENCES; MICROBIAL DIVERSITY; RARE BIOSPHERE; Science Technology - Other Topics; WRINKLES
Journal Title: PLoS One
Volume: 8
Issue: 6
ISSN: 1932-6203
Publisher: Public Library of Science  
Publication Place: SAN FRANCISCO; 1160 BATTERY STREET, STE 100, SAN FRANCISCO, CA 94111 USA
Date Published: 2013
Start Page: e66643
End Page: e66643
Language: English
DOI/URL:
Notes: PT: J; NR: 13; TC: 0; J9: PLOS ONE; PG: 6; GA: 177TH; UT: WOS:000321397800045