title: Falco: a quick and flexible single-cell RNA-seq processing framework on the cloud.
abstract: 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.
  
  
  
  Falco is available via a GNU General Public License at https://github.com/VCCRI/Falco/.
  
  
  
  j.ho@victorchang.edu.au.
  
  
  
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Victor Chang Cardiac Research Institute, Sydney, NSW, Australia.|St. Vincent's Clinical School, University of New South Wales, Sydney, NSW, Australia.
authors.forename: Andrian
authors.initials: A
authors.lastname: Yang
authors.affiliation: Victor Chang Cardiac Research Institute, Sydney, NSW, Australia.
authors.forename: Michael
authors.initials: M
authors.lastname: Troup
authors.affiliation: Victor Chang Cardiac Research Institute, Sydney, NSW, Australia.|St. Vincent's Clinical School, University of New South Wales, Sydney, NSW, Australia.
authors.forename: Peijie
authors.initials: P
authors.lastname: Lin
authors.affiliation: Victor Chang Cardiac Research Institute, Sydney, NSW, Australia.|St. Vincent's Clinical School, University of New South Wales, Sydney, NSW, Australia.
authors.forename: Joshua W K
authors.initials: JW
authors.lastname: Ho
mesh_terms: D000465:Algorithms; D000818:Animals; D019295:Computational Biology / Q000379:methods; D003713:Dendritic Cells / Q000378:metabolism; D015870:Gene Expression; D020869:Gene Expression Profiling / Q000379:methods*; D053263:Gene Regulatory Networks; D006801:Humans; D051379:Mice; D012313:RNA; D017423:Sequence Analysis, RNA / Q000379:methods*; D059010:Single-Cell Analysis / Q000379:methods*; D012984:Software
chemical_list: D012313:RNA