<?xml version="1.0" encoding="UTF-8"?><xml><records><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Olanda, Ricardo</style></author><author><style face="normal" font="default" size="100%">Pérez, Mariano</style></author><author><style face="normal" font="default" size="100%">Orduña, Juan M</style></author><author><style face="normal" font="default" size="100%">Tárraga, Joaquín</style></author><author><style face="normal" font="default" size="100%">Joaquín Dopazo</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">A new parallel pipeline for DNA methylation analysis of long reads datasets.</style></title><secondary-title><style face="normal" font="default" size="100%">BMC bioinformatics</style></secondary-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Methyl-Seq</style></keyword><keyword><style  face="normal" font="default" size="100%">NGS</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2017</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2017 Mar 09</style></date></pub-dates></dates><urls><web-urls><url><style face="normal" font="default" size="100%">http://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-017-1574-3</style></url></web-urls></urls><volume><style face="normal" font="default" size="100%">18</style></volume><pages><style face="normal" font="default" size="100%">161</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">BACKGROUND: DNA methylation is an important mechanism of epigenetic regulation in development and disease. New generation sequencers allow genome-wide measurements of the methylation status by reading short stretches of the DNA sequence (Methyl-seq). Several software tools for methylation analysis have been proposed over recent years. However, the current trend is that the new sequencers and the ones expected for an upcoming future yield sequences of increasing length, making these software tools inefficient and obsolete. RESULTS: In this paper, we propose a new software based on a strategy for methylation analysis of Methyl-seq sequencing data that requires much shorter execution times while yielding a better level of sensitivity, particularly for datasets composed of long reads. This strategy can be exported to other methylation, DNA and RNA analysis tools. CONCLUSIONS: The developed software tool achieves execution times one order of magnitude shorter than the existing tools, while yielding equal sensitivity for short reads and even better sensitivity for long reads.</style></abstract></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Tárraga, Joaquín</style></author><author><style face="normal" font="default" size="100%">Pérez, Mariano</style></author><author><style face="normal" font="default" size="100%">Orduña, Juan M</style></author><author><style face="normal" font="default" size="100%">Duato, José</style></author><author><style face="normal" font="default" size="100%">Medina, Ignacio</style></author><author><style face="normal" font="default" size="100%">Joaquín Dopazo</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">A Parallel and Sensitive Software Tool for Methylation Analysis on Multicore Platforms.</style></title><secondary-title><style face="normal" font="default" size="100%">Bioinformatics (Oxford, England)</style></secondary-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">BS-seq</style></keyword><keyword><style  face="normal" font="default" size="100%">HPC</style></keyword><keyword><style  face="normal" font="default" size="100%">methylation</style></keyword><keyword><style  face="normal" font="default" size="100%">NGS</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2015</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2015 Jun 10</style></date></pub-dates></dates><urls><web-urls><url><style face="normal" font="default" size="100%">http://bioinformatics.oxfordjournals.org/content/31/19/3130.long</style></url></web-urls></urls><number><style face="normal" font="default" size="100%">19</style></number><volume><style face="normal" font="default" size="100%">31</style></volume><pages><style face="normal" font="default" size="100%">3130-3138</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">MOTIVATION: 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 anonymous@clariano.uv.es (password &quot;anonymous&quot;). CONTACT: Juan.Orduna@uv.es.</style></abstract></record></records></xml>