A Review of Scalable Bioinformatics Pipelines

Abstract Scalability is increasingly important for bioinformatics analysis services, since these must handle larger datasets, more jobs, and more users. The pipelines used to implement analyses must therefore scale with respect to the resources on a single compute node, the number of nodes on a clus...

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Bibliographic Details
Main Authors:	Bjørn Fjukstad, Lars Ailo Bongo
Format:	Article
Language:	English
Published:	SpringerOpen 2017-10-01
Series:	Data Science and Engineering
Subjects:	Pipeline Bioinformatics Scalable Infrastructure Analysis services
Online Access:	http://link.springer.com/article/10.1007/s41019-017-0047-z

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spelling	doaj-5c2f1ab7a723413db24b467bcfabd2e72021-03-02T08:09:32ZengSpringerOpenData Science and Engineering2364-11852364-15412017-10-012324525110.1007/s41019-017-0047-zA Review of Scalable Bioinformatics PipelinesBjørn Fjukstad0Lars Ailo Bongo1Department of Computer Science, UiT The Arctic University of NorwayDepartment of Computer Science, UiT The Arctic University of NorwayAbstract Scalability is increasingly important for bioinformatics analysis services, since these must handle larger datasets, more jobs, and more users. The pipelines used to implement analyses must therefore scale with respect to the resources on a single compute node, the number of nodes on a cluster, and also to cost-performance. Here, we survey several scalable bioinformatics pipelines and compare their design and their use of underlying frameworks and infrastructures. We also discuss current trends for bioinformatics pipeline development.http://link.springer.com/article/10.1007/s41019-017-0047-zPipelineBioinformaticsScalableInfrastructureAnalysis services
collection	DOAJ
language	English
format	Article
sources	DOAJ
author	Bjørn Fjukstad Lars Ailo Bongo
spellingShingle	Bjørn Fjukstad Lars Ailo Bongo A Review of Scalable Bioinformatics Pipelines Data Science and Engineering Pipeline Bioinformatics Scalable Infrastructure Analysis services
author_facet	Bjørn Fjukstad Lars Ailo Bongo
author_sort	Bjørn Fjukstad
title	A Review of Scalable Bioinformatics Pipelines
title_short	A Review of Scalable Bioinformatics Pipelines
title_full	A Review of Scalable Bioinformatics Pipelines
title_fullStr	A Review of Scalable Bioinformatics Pipelines
title_full_unstemmed	A Review of Scalable Bioinformatics Pipelines
title_sort	review of scalable bioinformatics pipelines
publisher	SpringerOpen
series	Data Science and Engineering
issn	2364-1185 2364-1541
publishDate	2017-10-01
description	Abstract Scalability is increasingly important for bioinformatics analysis services, since these must handle larger datasets, more jobs, and more users. The pipelines used to implement analyses must therefore scale with respect to the resources on a single compute node, the number of nodes on a cluster, and also to cost-performance. Here, we survey several scalable bioinformatics pipelines and compare their design and their use of underlying frameworks and infrastructures. We also discuss current trends for bioinformatics pipeline development.
topic	Pipeline Bioinformatics Scalable Infrastructure Analysis services
url	http://link.springer.com/article/10.1007/s41019-017-0047-z
work_keys_str_mv	AT bjørnfjukstad areviewofscalablebioinformaticspipelines AT larsailobongo areviewofscalablebioinformaticspipelines AT bjørnfjukstad reviewofscalablebioinformaticspipelines AT larsailobongo reviewofscalablebioinformaticspipelines
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A Review of Scalable Bioinformatics Pipelines

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