@article {Busby018085, author = {Ben Busby and Allissa Dillman and Claire L. Simpson and Ian Fingerman and Sijung Yun and David M. Kristensen and Lisa Federer and Naisha Shah and Matthew C. LaFave and Laura Jimenez-Barron and Manjusha Pande and Wen Luo and Brendan Miller and Cem Mayden and Dhruva Chandramohan and Kipper Fletez-Brant and Paul W. Bible and Sergej Nowoshilow and Alfred Chan and Eric JC Galvez and Jeremy Chignell and Joseph N. Paulson and Manoj Kandpal and Suhyeon Yoon and Esther Asaki and Abhinav Nellore and Adam Stine and Robert Sanders and Jesse Becker and Matt Lesko and Mordechai Abzug and Eugene Yaschenko}, title = {Building Genomic Analysis Pipelines in a Hackathon Setting with Bioinformatician Teams: DNA-seq, Epigenomics, Metagenomics and RNA-seq}, elocation-id = {018085}, year = {2015}, doi = {10.1101/018085}, publisher = {Cold Spring Harbor Laboratory}, abstract = {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.}, URL = {https://www.biorxiv.org/content/early/2015/05/05/018085}, eprint = {https://www.biorxiv.org/content/early/2015/05/05/018085.full.pdf}, journal = {bioRxiv} }