gemBS: high throughput processing for DNA methylation data from bisulfite sequencing

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  • dc.contributor.author Merkel, Angelika
  • dc.contributor.author Fernández Callejo, Marcos
  • dc.contributor.author Casals, Eloi
  • dc.contributor.author Marco Sola, Santiago
  • dc.contributor.author Schuyler, Ronald P.
  • dc.contributor.author Gut, Ivo Glynne
  • dc.contributor.author Heath, Simon
  • dc.date.accessioned 2019-05-22T07:32:22Z
  • dc.date.issued 2019
  • dc.description.abstract Motivation: DNA methylation is essential for normal embryogenesis and development in mammals and can be captured at single base pair resolution by whole genome bisulfite sequencing (WGBS). Current available analysis tools are becoming rapidly outdated as they lack sensible functionality and efficiency to handle large amounts of data now commonly created. Results: We developed gemBS, a fast high-throughput bioinformatics pipeline specifically designed for large scale BS-Seq analysis that combines a high performance BS-mapper (GEM3) and a variant caller specifically for BS-Seq data (BScall). gemBS provides genotype information and methylation estimates for all genomic cytosines in different contexts (CpG and non-CpG) and a set of quality reports for comprehensive and reproducible analysis. gemBS is highly modular and can be easily automated, while producing robust and accurate results. Availability and implementation gemBS is released under the GNU GPLv3+ license. Source code and documentation are freely available from www.statgen.cat/gemBS. Supplementary information: Supplementary data are available at Bioinformatics online.
  • dc.format.mimetype application/pdf
  • dc.identifier.citation Merkel A, Fernández-Callejo M, Casals E, Marco-Sola S, Schuyler R, Gut IG, Heath SC. gemBS: high throughput processing for DNA methylation data from bisulfite sequencing. Bioinformatics. 2019; 35(5):737-742. DOI 10.1093/bioinformatics/bty690
  • dc.identifier.doi http://dx.doi.org/10.1093/bioinformatics/bty690
  • dc.identifier.issn 1367-4803
  • dc.identifier.uri http://hdl.handle.net/10230/37257
  • dc.language.iso eng
  • dc.publisher Oxford University Press
  • dc.relation.ispartof Bioinformatics. 2019; 35(5):737-742
  • dc.rights © Oxford University Press. This is a pre-copyedited, author-produced version of an article accepted for publication in Bioinformatics following peer review. The version of record Merkel A, Fernández-Callejo M, Casals E, Marco-Sola S, Schuyler R, Gut IG, Heath SC. gemBS: high throughput processing for DNA methylation data from bisulfite sequencing. Bioinformatics. 2019; 35(5):737-742. DOI 10.1093/bioinformatics/bty690 is available online at: https://academic.oup.com/bioinformatics/article/35/5/737/5077236 and http://dx.doi.org/10.1093/bioinformatics/bty690.
  • dc.rights.accessRights info:eu-repo/semantics/openAccess
  • dc.title gemBS: high throughput processing for DNA methylation data from bisulfite sequencing
  • dc.type info:eu-repo/semantics/article
  • dc.type.version info:eu-repo/semantics/acceptedVersion

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