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- Title
Cloud accelerated alignment and assembly of full-length single-cell RNA-seq data using Falco.
- Authors
Yang, Andrian; Kishore, Abhinav; Phipps, Benjamin; Ho, Joshua W. K.
- Abstract
Background: Read alignment and transcript assembly are the core of RNA-seq analysis for transcript isoform discovery. Nonetheless, current tools are not designed to be scalable for analysis of full-length bulk or single cell RNA-seq (scRNA-seq) data. The previous version of our cloud-based tool Falco only focuses on RNA-seq read counting, but does not allow for more flexible steps such as alignment and read assembly. Results: The Falco framework can harness the parallel and distributed computing environment in modern cloud platforms to accelerate read alignment and transcript assembly of full-length bulk RNA-seq and scRNA-seq data. There are two new modes in Falco: alignment-only and transcript assembly. In the alignment-only mode, Falco can speed up the alignment process by 2.5–16.4x based on two public scRNA-seq datasets when compared to alignment on a highly optimised standalone computer. Furthermore, it also provides a 10x average speed-up compared to alignment using published cloud-enabled tool for read alignment, Rail-RNA. In the transcript assembly mode, Falco can speed up the transcript assembly process by 1.7–16.5x compared to performing transcript assembly on a highly optimised computer. Conclusion: Falco is a significantly updated open source big data processing framework that enables scalable and accelerated alignment and assembly of full-length scRNA-seq data on the cloud. The source code can be found at https://github.com/VCCRI/Falco.
- Subjects
BIG data; ELECTRONIC data processing; SOURCE code; PARALLEL programming; DATA; STATIC random access memory
- Publication
BMC Genomics, 2019, Vol 20, p1
- ISSN
1471-2164
- Publication type
Article
- DOI
10.1186/s12864-019-6341-6