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 Vivian, John
A1 Rao, Arjun
A1 Nothaft, Frank Austin
A1 Ketchum, Christopher
A1 Armstrong, Joel
A1 Novak, Adam
A1 Pfeil, Jacob
A1 Narkizian, Jake
A1 Deran, Alden D.
A1 Musselman-Brown, Audrey
A1 Schmidt, Hannes
A1 Amstutz, Peter
A1 Craft, Brian
A1 Goldman, Mary
A1 Rosenbloom, Kate
A1 Cline, Melissa
A1 O’Connor, Brian
A1 Hanna, Megan
A1 Birger, Chet
A1 Kent, W. James
A1 Patterson, David A.
A1 Joseph, Anthony D.
A1 Zhu, Jingchun
A1 Zaranek, Sasha
A1 Getz, Gad
A1 Haussler, David
A1 Paten, Benedict
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.