Angelika Merkel1, Marcos Fernández-Callejo1, Eloi Casals1, Santiago Marco-Sola2, Ronald Schuyler3, Ivo G Gut1,4, Simon C Heath1,4. 1. Centro Nacional de Análisis Genómico (CNAG-CRG), Centre de Regulacio Genómico (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain. 2. Universitat Autònoma de Barcelona, Bellaterra, Spain. 3. Department of Immunology and Microbiology, University of Colorado, Aurora, CO, USA. 4. Universitat Pompeu Fabra (UPF), Barcelona, Spain.
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 Current available analysis tools are becoming rapidly outdated as they lack sensible functionality and efficiency to handle large amounts of data now commonly created.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.
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 Current available analysis tools are becoming rapidly outdated as they lack sensible functionality and efficiency to handle large amounts of data now commonly created.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.
Authors: Diana Buitrago; Mireia Labrador; Juan Pablo Arcon; Rafael Lema; Oscar Flores; Anna Esteve-Codina; Julie Blanc; Nuria Villegas; David Bellido; Marta Gut; Pablo D Dans; Simon C Heath; Ivo G Gut; Isabelle Brun Heath; Modesto Orozco Journal: Nat Commun Date: 2021-05-28 Impact factor: 14.919
Authors: Lukas F K Kuderna; Esther Lizano; Eva Julià; Jessica Gomez-Garrido; Aitor Serres-Armero; Martin Kuhlwilm; Regina Antoni Alandes; Marina Alvarez-Estape; David Juan; Heath Simon; Tyler Alioto; Marta Gut; Ivo Gut; Mikkel Heide Schierup; Oscar Fornas; Tomas Marques-Bonet Journal: Nat Commun Date: 2019-01-02 Impact factor: 14.919