Yang, Andrian and Kishore, Abhinav and Phipps, Benjamin and Ho, Joshua W. K. (2019) Cloud accelerated alignment and assembly of full-length single-cell RNA-seq data using Falco. BMC Genomics, 20 (S10). ISSN 1471-2164
Full text not available from this repository.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.
| Item Type: | Article |
|---|---|
| Subjects: | R Medicine > R Medicine (General) |
| Depositing User: | Repository Administrator |
| Date Deposited: | 23 Jan 2020 04:19 |
| Last Modified: | 23 Jan 2020 04:19 |
| URI: | https://eprints.victorchang.edu.au/id/eprint/916 |
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