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BMC Bioinformatics

, 15:337

Sequence analysis applications

Abstract

BackgroundDNA methylation changes are associated with a wide array of biological processes. Bisulfite conversion of DNA followed by high-throughput sequencing is increasingly being used to assess genome-wide methylation at single-base resolution. The relative slowness of most commonly used aligners for processing such data introduces an unnecessarily long delay between receipt of raw data and statistical analysis. While this process can be sped-up by using computer clusters, current tools are not designed with them in mind and end-users must create such implementations themselves.

ResultsHere, we present a novel BS-seq aligner, Bison, which exploits multiple nodes of a computer cluster to speed up this process and also has increased accuracy. Bison is accompanied by a variety of helper programs and scripts to ease, as much as possible, the process of quality control and preparing results for statistical analysis by a variety of popular R packages. Bison is also accompanied by bison herd, a variant of Bison with the same output but that can scale to a semi-arbitrary number of nodes, with concomitant increased demands on the underlying message passing interface implementation.

ConclusionsBison is a new bisulfite-converted short-read aligner providing end users easier scalability for performance gains, more accurate alignments, and a convenient pathway for quality controlling alignments and converting methylation calls into a form appropriate for statistical analysis. Bison and the more scalable bison herd are natively able to utilize multiple nodes of a computer cluster simultaneously and serve to simplify to the process of creating analysis pipelines.

KeywordsDNA Methylation Alignment Bisulfite sequencing Computer cluster Electronic supplementary materialThe online version of this article doi:10.1186-1471-2105-15-337 contains supplementary material, which is available to authorized users.

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Author: Devon Patrick Ryan - Dan Ehninger

Source: https://link.springer.com/







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