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PBHoney: identifying genomic variants via long-read discordance and interrupted mapping

Adam C English*, William J Salerno and Jeffrey G Reid

Author Affiliations

Human Genome Sequencing Center at Baylor College of Medicine, One Baylor Plaza, Houston 77030, Texas, USA

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BMC Bioinformatics 2014, 15:180  doi:10.1186/1471-2105-15-180

Published: 10 June 2014

Abstract

Background

As resequencing projects become more prevalent across a larger number of species, accurate variant identification will further elucidate the nature of genetic diversity and become increasingly relevant in genomic studies. However, the identification of larger genomic variants via DNA sequencing is limited by both the incomplete information provided by sequencing reads and the nature of the genome itself. Long-read sequencing technologies provide high-resolution access to structural variants often inaccessible to shorter reads.

Results

We present PBHoney, software that considers both intra-read discordance and soft-clipped tails of long reads (>10,000 bp) to identify structural variants. As a proof of concept, we identify four structural variants and two genomic features in a strain of Escherichia coli with PBHoney and validate them via de novo assembly. PBHoney is available for download at http://sourceforge.net/projects/pb-jelly/ webcite.

Conclusions

Implementing two variant-identification approaches that exploit the high mappability of long reads, PBHoney is demonstrated as being effective at detecting larger structural variants using whole-genome Pacific Biosciences RS II Continuous Long Reads. Furthermore, PBHoney is able to discover two genomic features: the existence of Rac-Phage in isolate; evidence of E. coli’s circular genome.

Keywords:
Structural variation; Sequencing; PacificBiosciences