A Parallel and Sensitive Software Tool for Methylation Analysis on Multicore Platforms.

TitleA Parallel and Sensitive Software Tool for Methylation Analysis on Multicore Platforms.
Publication TypeJournal Article
Year of Publication2015
AuthorsTárraga J, Pérez M, Orduña JM, Duato J, Medina I, Dopazo J
Journal TitleBioinformatics (Oxford, England)
Volume31
Issue19
Pages3130-3138
Journal Date2015 Jun 10
ISSN1367-4811
KeywordsBS-seq, HPC, methylation, NGS
AbstractMOTIVATION: DNA methylation analysis suffers from very long processing time, since the advent of Next-Generation Sequencers (NGS) has shifted the bottleneck of genomic studies from the sequencers that obtain the DNA samples to the software that performs the analysis of these samples. The existing software for methylation analysis does not seem to scale efficiently neither with the size of the dataset nor with the length of the reads to be analyzed. Since it is expected that the sequencers will provide longer and longer reads in the near future, efficient and scalable methylation software should be developed. RESULTS: We present a new software tool, called HPG-Methyl, which efficiently maps bisulfite sequencing reads on DNA, analyzing DNA methylation. The strategy used by this software consists of leveraging the speed of the Burrows-Wheeler Transform to map a large number of DNA fragments (reads) rapidly, as well as the accuracy of the Smith-Waterman algorithm, which is exclusively employed to deal with the most ambiguous and shortest reads. Experimental results on platforms with Intel multicore processors show that HPGMethyl significantly outperforms in both execution time and sensitivity state-of-the-art software such as Bismark, BS-Seeker or BSMAP, particularly for long bisulfite reads. AVAILABILITY: Software in the form of C libraries and functions, together with instructions to compile and execute this software. Available by sftp to anonymousatclariano [dot] uv [dot] es (password "anonymous"). CONTACT: Juan [dot] Ordunaatuv [dot] es.
URLhttp://bioinformatics.oxfordjournals.org/content/31/19/3130.long
DOI10.1093/bioinformatics/btv357
Alternate JournalBioinformatics