Churchill: an ultra-fast,deterministic, highly scalable and balanced parallelization strategy for the discovery of human genetic variation in clinical and population-scale genomics |
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| Authors: | Benjamin J Kelly James R Fitch Yangqiu Hu Donald J Corsmeier Huachun Zhong Amy N Wetzel Russell D Nordquist David L Newsom Peter White |
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| Affiliation: | Center for Microbial Pathogenesis, The Research Institute at Nationwide Children’s Hospital, 700 Children’s Drive, Columbus, OH 43205 USA ;Department of Pediatrics, College of Medicine, The Ohio State University, Columbus, Ohio USA |
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| Abstract: | While advances in genome sequencing technology make population-scale genomics a possibility, current approaches for analysis of these data rely upon parallelization strategies that have limited scalability, complex implementation and lack reproducibility. Churchill, a balanced regional parallelization strategy, overcomes these challenges, fully automating the multiple steps required to go from raw sequencing reads to variant discovery. Through implementation of novel deterministic parallelization techniques, Churchill allows computationally efficient analysis of a high-depth whole genome sample in less than two hours. The method is highly scalable, enabling full analysis of the 1000 Genomes raw sequence dataset in a week using cloud resources. http://churchill.nchri.org/.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-014-0577-x) contains supplementary material, which is available to authorized users. |
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