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

作者：Eren A Murat; Vineis Joseph H; Morrison Hilary G; Sogin Mitchell L^*

来源：PLos One, 2013, 8(6): e66643.

DOI：10.1371/journal.pone.0066643

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.

• 出版日期2013-6-17