NGSmethDB 2017: enhanced methylomes and differential methylation Lebrón, Ricardo Gómez Martín, Cristina Carpena, Pedro Bernaola-Galván, Pedro Barturen, Guillermo Hackenberg, Michael Oliver Jiménez, José Lutgardo Methylomes Methylation DNA The 2017 update of NGSmethDB stores whole genome methylomes generated from short-read data sets obtained by bisulfite sequencing (WGBS) technology. To generate high-quality methylomes, stringent quality controls were integrated with third-part software, adding also a two-step mapping process to exploit the advantages of the new genome assembly models. The samples were all profiled under constant parameter settings, thus enabling comparative downstream analyses. Besides a significant increase in the number of samples, NGSmethDB now includes two additional data-types, which are a valuable resource for the discovery of methylation epigenetic biomarkers: (i) differentially methylated single-cytosines; and (ii) methylation segments (i.e. genome regions of homogeneous methylation). The NGSmethDB back-end is now based on MongoDB, a NoSQL hierarchical database using JSONformatted documents and dynamic schemas, thus accelerating sample comparative analyses. Besides conventional database dumps, track hubs were implemented, which improved database access, visualization in genome browsers and comparative analyses to third-part annotations. In addition, the database can be also accessed through a RESTful API. Lastly, a Python client and a multiplatform virtual machine allow for program-driven access from user desktop. This way, private methylation data can be compared to NGSmethDB without the need to upload them to public servers. Database website: http://bioinfo2.ugr.es/NGSmethDB. 2026-02-09T11:53:19Z 2026-02-09T11:53:19Z 2017-01 journal article Lebrón R, Gómez-Martín C, Carpena P, Bernaola-Galván P, Barturen G, Hackenberg M, Oliver JL. NGSmethDB 2017: enhanced methylomes and differential methylation. Nucleic Acids Res. 2017 Jan 4;45(D1):D97-D103. doi: 10.1093/nar/gkw996 1362-4962 https://hdl.handle.net/10481/110767 10.1093/nar/gkw996 eng http://creativecommons.org/licenses/by-nc-nd/4.0/ open access Creative Commons Attribution-NonCommercial-NoDerivs 3.0 License Attribution-NonCommercial-NoDerivatives 4.0 Internacional Oxford Academic