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Falco: A quick and flexible single-cell RNA-seq processing framework on the cloud

Andrian Yang, Michael Troup, Peijie Lin, Joshua W. K. Ho
doi: https://doi.org/10.1101/064006
Andrian Yang
1Victor Chang Cardiac Research Institute, Sydney, NSW, Australia
2St. Vincent’s Clinical School, University of New South Wales, Sydney, NSW, Australia
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Michael Troup
1Victor Chang Cardiac Research Institute, Sydney, NSW, Australia
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Peijie Lin
1Victor Chang Cardiac Research Institute, Sydney, NSW, Australia
2St. Vincent’s Clinical School, University of New South Wales, Sydney, NSW, Australia
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Joshua W. K. Ho
1Victor Chang Cardiac Research Institute, Sydney, NSW, Australia
2St. Vincent’s Clinical School, University of New South Wales, Sydney, NSW, Australia
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Abstract

Summary Single-cell RNA-seq (scRNA-seq) is increasingly used in a range of biomedical studies. Nonetheless, current RNA-seq analysis tools are not specifically designed to efficiently process scRNA-seq data due to their limited scalability. Here we introduce Falco, a cloud-based framework to enable paralellisation of existing RNA-seq processing pipelines using big data technologies of Apache Hadoop and Apache Spark for performing massively parallel analysis of large scale transcriptomic data. Using two public scRNA-seq data sets and two popular RNA-seq alignment/feature quantification pipelines, we show that the same processing pipeline runs 2.6 – 145.4 times faster using Falco than running on a highly optimised single node analysis. Falco also allows user to the utilise low-cost spot instances of Amazon Web Services (AWS), providing a 65% reduction in cost of analysis.

Availability Falco is available via a GNU General Public License at https://github.com/VCCRI/Falco/

Contact j.ho{at}victorchang.edu.au

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted October 27, 2016.
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Falco: A quick and flexible single-cell RNA-seq processing framework on the cloud
Andrian Yang, Michael Troup, Peijie Lin, Joshua W. K. Ho
bioRxiv 064006; doi: https://doi.org/10.1101/064006
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Falco: A quick and flexible single-cell RNA-seq processing framework on the cloud
Andrian Yang, Michael Troup, Peijie Lin, Joshua W. K. Ho
bioRxiv 064006; doi: https://doi.org/10.1101/064006

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