Recommendations on e-infrastructures for next-generation sequencing

Spjuth, Ola (author): Uppsala universitet,Institutionen för farmaceutisk biovetenskap,Science for Life Laboratory, SciLifeLab

Bongcam Rudloff, Erik (author): Swedish University of Agricultural Sciences,Sveriges lantbruksuniversitet,Institutionen för husdjursgenetik (HGEN),Department of Animal Breeding and Genetics

Dahlberg, Johan (author): Uppsala universitet,Institutionen för medicinska vetenskaper

Dahlö, Martin (author): Uppsala universitet,Institutionen för informationsteknologi,Cancerfarmakologi och beräkningsmedicin

Kallio, Aleksi (author)

Pireddu, Luca (author)

Vezzi, Francesco (author): Stockholms universitet,Institutionen för biokemi och biofysik,Science for Life Laboratory (SciLifeLab)

Korpelainen, Eija (author)

(creator_code:org_t)

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Abstract Subject headings

With ever-increasing amounts of data being produced by next-generation sequencing (NGS) experiments, the requirements placed on supporting e-infrastructures have grown. In this work, we provide recommendations based on the collective experiences from participants in the EU COST Action SeqAhead for the tasks of data preprocessing, upstream processing, data delivery, and downstream analysis, as well as long-term storage and archiving. We cover demands on computational and storage resources, networks, software stacks, automation of analysis, education, and also discuss emerging trends in the field. E-infrastructures for NGS require substantial effort to set up and maintain over time, and with sequencing technologies and best practices for data analysis evolving rapidly it is important to prioritize both processing capacity and e-infrastructure flexibility when making strategic decisions to support the data analysis demands of tomorrow. Due to increasingly demanding technical requirements we recommend that e-infrastructure development and maintenance be handled by a professional service unit, be it internal or external to the organization, and emphasis should be placed on collaboration between researchers and IT professionals.

NATURVETENSKAP -- Biologi (hsv//swe)
NATURAL SCIENCES -- Biological Sciences (hsv//eng)
NATURVETENSKAP -- Data- och informationsvetenskap -- Bioinformatik (hsv//swe)
NATURAL SCIENCES -- Computer and Information Sciences -- Bioinformatics (hsv//eng)
NATURVETENSKAP -- Biologi -- Bioinformatik och systembiologi (hsv//swe)
NATURAL SCIENCES -- Biological Sciences -- Bioinformatics and Systems Biology (hsv//eng)

By the author/editor: Spjuth, Ola; Bongcam Rudloff, ...; Dahlberg, Johan; Dahlö, Martin; Kallio, Aleksi; Pireddu, Luca; show more...; Vezzi, Francesco; Korpelainen, Eij ...; show less...

About the subject

NATURAL SCIENCES: NATURAL SCIENCES; and Computer and Inf ...; and Bioinformatics

NATURAL SCIENCES: NATURAL SCIENCES; and Biological Scien ...; and Bioinformatics a ...

By the university: Stockholm University; Uppsala University; Swedish University of Agricultural Sciences

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