RT Journal Article
SR Electronic
T1 Rapid and efficient analysis of 20,000 RNA-seq samples with Toil
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 062497
DO 10.1101/062497
A1 John Vivian
A1 Arjun Rao
A1 Frank Austin Nothaft
A1 Christopher Ketchum
A1 Joel Armstrong
A1 Adam Novak
A1 Jacob Pfeil
A1 Jake Narkizian
A1 Alden D. Deran
A1 Audrey Musselman-Brown
A1 Hannes Schmidt
A1 Peter Amstutz
A1 Brian Craft
A1 Mary Goldman
A1 Kate Rosenbloom
A1 Melissa Cline
A1 Brian O’Connor
A1 Megan Hanna
A1 Chet Birger
A1 W. James Kent
A1 David A. Patterson
A1 Anthony D. Joseph
A1 Jingchun Zhu
A1 Sasha Zaranek
A1 Gad Getz
A1 David Haussler
A1 Benedict Paten
YR 2016
UL http://biorxiv.org/content/early/2016/07/07/062497.abstract
AB 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.