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Article: Cloud accelerated alignment and assembly of full-length single-cell RNA-seq data using Falco

TitleCloud accelerated alignment and assembly of full-length single-cell RNA-seq data using Falco
Authors
KeywordsSingle-cell RNA-seq
Cloud computing
Falco
Alignment
Transcript assembly
Issue Date2019
PublisherBioMed Central Ltd. The Journal's web site is located at http://www.biomedcentral.com/bmcgenomics/
Citation
BMC Genomics, 2019, v. 20, p. article no. 927 How to Cite?
AbstractBackground: 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.
Persistent Identifierhttp://hdl.handle.net/10722/282037
ISSN
2023 Impact Factor: 3.5
2023 SCImago Journal Rankings: 1.047
PubMed Central ID
ISI Accession Number ID

 

DC FieldValueLanguage
dc.contributor.authorYang, A-
dc.contributor.authorKishore, A-
dc.contributor.authorPhipps, B-
dc.contributor.authorHo, JWK-
dc.date.accessioned2020-04-19T03:34:28Z-
dc.date.available2020-04-19T03:34:28Z-
dc.date.issued2019-
dc.identifier.citationBMC Genomics, 2019, v. 20, p. article no. 927-
dc.identifier.issn1471-2164-
dc.identifier.urihttp://hdl.handle.net/10722/282037-
dc.description.abstractBackground: 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.-
dc.languageeng-
dc.publisherBioMed Central Ltd. The Journal's web site is located at http://www.biomedcentral.com/bmcgenomics/-
dc.relation.ispartofBMC Genomics-
dc.rightsBMC Genomics. Copyright © BioMed Central Ltd.-
dc.rightsThis work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.-
dc.subjectSingle-cell RNA-seq-
dc.subjectCloud computing-
dc.subjectFalco-
dc.subjectAlignment-
dc.subjectTranscript assembly-
dc.titleCloud accelerated alignment and assembly of full-length single-cell RNA-seq data using Falco-
dc.typeArticle-
dc.identifier.emailHo, JWK: jwkho@hku.hk-
dc.identifier.authorityHo, JWK=rp02436-
dc.description.naturepublished_or_final_version-
dc.identifier.doi10.1186/s12864-019-6341-6-
dc.identifier.pmid31888474-
dc.identifier.pmcidPMC6936136-
dc.identifier.scopuseid_2-s2.0-85077211844-
dc.identifier.hkuros309735-
dc.identifier.volume20-
dc.identifier.spagearticle no. 927-
dc.identifier.epagearticle no. 927-
dc.identifier.isiWOS:000508013000003-
dc.publisher.placeUnited Kingdom-
dc.identifier.issnl1471-2164-

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