Rapid and efficient analysis of 20,000 RNA-seq samples with Toil
Frank Austin Nothaft,
Alden D. Deran,
W. James Kent,
David A. Patterson,
Anthony D. Joseph,
Posted 07 Jul 2016
bioRxiv DOI: 10.1101/062497 (published DOI: 10.1038/nbt.3772)
Posted 07 Jul 2016
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.
- Downloaded 6,214 times
- Download rankings, all-time:
- Site-wide: 535 out of 92,062
- In bioinformatics: 82 out of 8,636
- Year to date:
- Site-wide: 10,331 out of 92,062
- Since beginning of last month:
- Site-wide: 6,633 out of 92,062
Downloads over time
Distribution of downloads per paper, site-wide
- 18 Dec 2019: We're pleased to announce PanLingua, a new tool that enables you to search for machine-translated bioRxiv preprints using more than 100 different languages.
- 21 May 2019: PLOS Biology has published a community page about Rxivist.org and its design.
- 10 May 2019: The paper analyzing the Rxivist dataset has been published at eLife.
- 1 Mar 2019: We now have summary statistics about bioRxiv downloads and submissions.
- 8 Feb 2019: Data from Altmetric is now available on the Rxivist details page for every preprint. Look for the "donut" under the download metrics.
- 30 Jan 2019: preLights has featured the Rxivist preprint and written about our findings.
- 22 Jan 2019: Nature just published an article about Rxivist and our data.
- 13 Jan 2019: The Rxivist preprint is live!