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:10.1093/bioinformatics/btw732

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

Bioinformatics. 2017 Mar 1;33(5):767-769. doi: 10.1093/bioinformatics/btw732.

Authors

Andrian Yang^{1

2}, Michael Troup¹, Peijie Lin^{1

2}, Joshua W K Ho^{1

2}

Affiliations

¹ Victor Chang Cardiac Research Institute, Sydney, NSW, Australia.
² St. Vincent's Clinical School, University of New South Wales, Sydney, NSW, Australia.

PMID: 28025200
DOI: 10.1093/bioinformatics/btw732

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 paralellization 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 datasets 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 optimized standalone computer. Falco also allows users to utilize low-cost spot instances of Amazon Web Services, providing a ∼65% reduction in cost of analysis.

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

Contact: j.ho@victorchang.edu.au.

Supplementary information: Supplementary data are available at Bioinformatics online.

MeSH terms

Algorithms
Animals
Computational Biology / methods
Dendritic Cells / metabolism
Gene Expression
Gene Expression Profiling / methods*
Gene Regulatory Networks*
Humans
Mice
RNA
Sequence Analysis, RNA / methods*
Single-Cell Analysis / methods*
Software*

Substances

RNA