bioRxivBioinformatics
Rapid and efficient analysis of 20,000 RNA-seq samples with Toil
John VivianiD, Arjun Rao, Frank Austin NothaftiD, Christopher Ketchum, Joel Armstrong, Adam Novak, Jacob PfeiliD, Jake Narkizian, Alden D. Deran, Audrey Musselman-Brown, Hannes Schmidt, Peter Amstutz, Brian CraftiD, Mary Goldman, Kate Rosenbloom, Melissa Cline, Brian O'Connor, Megan Hanna, Chet Birger, W. James Kent, David A. Patterson, Anthony D. JosephiD, Jingchun ZhuiD, Sasha Zaranek, Gad Getz, , Benedict PateniD
Abstract
Toil is portable, open-source workflow software that supports contemporary workflow definition languages and can be used to securely and reproducibly run scientific workflows efficiently at large-scale. To demonstrate Toil, we processed over 20,000 RNA-seq samples to create a consistent meta-analysis of five datasets free of computational batch effects that we make freely available. Nearly all the samples were analysed in under four days using a commercial cloud cluster of 32,000 preemptable cores.
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