TY - JOUR T1 - Building Genomic Analysis Pipelines in a Hackathon Setting with Bioinformatician Teams: DNA-seq, Epigenomics, Metagenomics and RNA-seq JF - bioRxiv DO - 10.1101/018085 SP - 018085 AU - Ben Busby AU - Allissa Dillman AU - Claire L. Simpson AU - Ian Fingerman AU - Sijung Yun AU - David M. Kristensen AU - Lisa Federer AU - Naisha Shah AU - Matthew C. LaFave AU - Laura Jimenez-Barron AU - Manjusha Pande AU - Wen Luo AU - Brendan Miller AU - Cem Mayden AU - Dhruva Chandramohan AU - Kipper Fletez-Brant AU - Paul W. Bible AU - Sergej Nowoshilow AU - Alfred Chan AU - Eric JC Galvez AU - Jeremy Chignell AU - Joseph N. Paulson AU - Manoj Kandpal AU - Suhyeon Yoon AU - Esther Asaki AU - Abhinav Nellore AU - Adam Stine AU - Robert Sanders AU - Jesse Becker AU - Matt Lesko AU - Mordechai Abzug AU - Eugene Yaschenko Y1 - 2015/01/01 UR - http://biorxiv.org/content/early/2015/05/05/018085.abstract N2 - We assembled teams of genomics professionals to assess whether we could rapidly develop pipelines to answer biological questions commonly asked by biologists and others new to bioinformatics by facilitating analysis of high-throughput sequencing data. In January 2015, teams were assembled on the National Institutes of Health (NIH) campus to address questions in the DNA-seq, epigenomics, metagenomics and RNA-seq subfields of genomics. The only two rules for this hackathon were that either the data used were housed at the National Center for Biotechnology Information (NCBI) or would be submitted there by a participant in the next six months, and that all software going into the pipeline was open-source or open-use. Questions proposed by organizers, as well as suggested tools and approaches, were distributed to participants a few days before the event and were refined during the event. Pipelines were published on GitHub, a web service providing publicly available, free-usage tiers for collaborative software development (https://github.com/features/). The code was published at https://github.com/DCGenomics/ with separate repositories for each team, starting with hackathon_v001. ER -