Building Genomic Analysis Pipelines in a Hackathon Setting with Bioinformatician Teams: DNA-seq, Epigenomics, Metagenomics and RNA-seq

• DOI: 10.1101/018085
• Publication Date: 2015-04-17T05:05:41Z
• Authors: Ben Busby; Allissa Dillman; Claire L. Simpson; Ian Fingerman; Sijung Yun; David M. Kristensen; Lisa Federer; Naisha Shah; Matthew C. LaFave; Laura Jimenez-Barron; Manjusha Pande; Wen Luo; Brendan Miller; Cem Mayden; Dhruva Chandramohan; Kipper Fletez-Brant; Paul W. Bible; Sergej Nowoshilow; Alfred Chan; Eric JC Galvez; Jeremy Chignell; Joseph N. Paulson; Manoj Kandpal; Suhyeon Yoon; Esther Asaki; Abhinav Nellore; Adam Stine; Robert Sanders; Jesse Becker; Matt Lesko; Mordechai Abzug; Eugene Yaschenko
• Keywords: RNA-Seq; Epigenomics

Abstract We assembled teams of genomics professionals to assess whether we could rapidly develop pipelines answer biological questions commonly asked by biologists and others new bioinformatics facilitating analysis high-throughput sequencing data. In January 2015, were on the National Institutes Health (NIH) campus address in DNA-seq, epigenomics, metagenomics RNA-seq subfields genomics. The only two rules for this hackathon that either data used housed at Center Biotechnology Information (NCBI) or would be submitted there a participant next six months, all software going into pipeline was open-source open-use. Questions proposed organizers, as well suggested tools approaches, distributed participants few days before event refined during event. Pipelines published GitHub, web service providing publicly available, free-usage tiers collaborative development ( https://github.com/features/ ). code https://github.com/DCGenomics/ with separate repositories each team, starting hackathon_v001.