Htsget: A protocol for securely streaming genomic data

Jerome Kelleher; Mike Lin; C. H. Albach; Ewan Birney; Robert Davies; Marina Gourtovaia; David Glazer; Cristina Y. Gonzalez; David K. Jackson; Aaron Kemp; John Marshall; Andrew Nowak; Alexander Senf; Jaime M. Tovar-Corona; Alexander Vikhorev; Thomas M. Keane; Dixie Baker; Vadim Zalunin; Angel Pizarro; Richard Durbin; Mark Diekhans; Edmon Begoli; Ilia Tulchinsky; Heng Li; Rishi Nag; Stephen Keenan; Ilkka Lappalainen; Jim Robinson

doi:10.1093/bioinformatics/bty492

Htsget: A protocol for securely streaming genomic data

Jerome Kelleher
, Mike Lin
, C. H. Albach
, Ewan Birney
, Robert Davies
, Marina Gourtovaia
, David Glazer
, Cristina Y. Gonzalez
, David K. Jackson
, Aaron Kemp
, John Marshall
, Andrew Nowak
, Alexander Senf
, Jaime M. Tovar-Corona
, Alexander Vikhorev
, Thomas M. Keane
, Dixie Baker
, Vadim Zalunin
, Angel Pizarro
, Richard Durbin

Mark Diekhans, Edmon Begoli, Ilia Tulchinsky, Heng Li, Rishi Nag, Stephen Keenan, Ilkka Lappalainen, Jim Robinson

Computational Sciences & Engineering Div

Research output: Contribution to journal › Article › peer-review

20 Scopus citations

Abstract

Standardized interfaces for efficiently accessing high-throughput sequencing data are a fundamental requirement for large-scale genomic data sharing. We have developed htsget, a protocol for secure, efficient and reliable access to sequencing read and variation data. We demonstrate four independent client and server implementations, and the results of a comprehensive interoperability demonstration. Availability and implementation http://samtools.github.io/hts-specs/htsget.html.

Original language	English
Pages (from-to)	119-121
Number of pages	3
Journal	Bioinformatics
Volume	35
Issue number	1
DOIs	https://doi.org/10.1093/bioinformatics/bty492
State	Published - Jan 1 2019

Funding

This work was supported by the Wellcome Trust [100956/Z/13/Z][201535/ Z/16/Z].

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Kelleher, J., Lin, M., Albach, C. H., Birney, E., Davies, R., Gourtovaia, M., Glazer, D., Gonzalez, C. Y., Jackson, D. K., Kemp, A., Marshall, J., Nowak, A., Senf, A., Tovar-Corona, J. M., Vikhorev, A., Keane, T. M., Baker, D., Zalunin, V., Pizarro, A., ... Robinson, J. (2019). Htsget: A protocol for securely streaming genomic data. Bioinformatics, 35(1), 119-121. https://doi.org/10.1093/bioinformatics/bty492

@article{f57058c983404ba9816694553fc2ebe4,

title = "Htsget: A protocol for securely streaming genomic data",

abstract = "Standardized interfaces for efficiently accessing high-throughput sequencing data are a fundamental requirement for large-scale genomic data sharing. We have developed htsget, a protocol for secure, efficient and reliable access to sequencing read and variation data. We demonstrate four independent client and server implementations, and the results of a comprehensive interoperability demonstration. Availability and implementation http://samtools.github.io/hts-specs/htsget.html.",

author = "Jerome Kelleher and Mike Lin and Albach, \{C. H.\} and Ewan Birney and Robert Davies and Marina Gourtovaia and David Glazer and Gonzalez, \{Cristina Y.\} and Jackson, \{David K.\} and Aaron Kemp and John Marshall and Andrew Nowak and Alexander Senf and Tovar-Corona, \{Jaime M.\} and Alexander Vikhorev and Keane, \{Thomas M.\} and Dixie Baker and Vadim Zalunin and Angel Pizarro and Richard Durbin and Mark Diekhans and Edmon Begoli and Ilia Tulchinsky and Heng Li and Rishi Nag and Stephen Keenan and Ilkka Lappalainen and Jim Robinson",

note = "Publisher Copyright: {\textcopyright} 2018 The Author(s). Published by Oxford University Press.",

year = "2019",

month = jan,

day = "1",

doi = "10.1093/bioinformatics/bty492",

language = "English",

volume = "35",

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Kelleher, J, Lin, M, Albach, CH, Birney, E, Davies, R, Gourtovaia, M, Glazer, D, Gonzalez, CY, Jackson, DK, Kemp, A, Marshall, J, Nowak, A, Senf, A, Tovar-Corona, JM, Vikhorev, A, Keane, TM, Baker, D, Zalunin, V, Pizarro, A, Durbin, R, Diekhans, M, Begoli, E, Tulchinsky, I, Li, H, Nag, R, Keenan, S, Lappalainen, I & Robinson, J 2019, 'Htsget: A protocol for securely streaming genomic data', Bioinformatics, vol. 35, no. 1, pp. 119-121. https://doi.org/10.1093/bioinformatics/bty492

TY - JOUR

T1 - Htsget

T2 - A protocol for securely streaming genomic data

AU - Kelleher, Jerome

AU - Lin, Mike

AU - Albach, C. H.

AU - Birney, Ewan

AU - Davies, Robert

AU - Gourtovaia, Marina

AU - Glazer, David

AU - Gonzalez, Cristina Y.

AU - Jackson, David K.

AU - Kemp, Aaron

AU - Marshall, John

AU - Nowak, Andrew

AU - Senf, Alexander

AU - Tovar-Corona, Jaime M.

AU - Vikhorev, Alexander

AU - Keane, Thomas M.

AU - Baker, Dixie

AU - Zalunin, Vadim

AU - Pizarro, Angel

AU - Durbin, Richard

AU - Diekhans, Mark

AU - Begoli, Edmon

AU - Tulchinsky, Ilia

AU - Li, Heng

AU - Nag, Rishi

AU - Keenan, Stephen

AU - Lappalainen, Ilkka

AU - Robinson, Jim

PY - 2019/1/1

Y1 - 2019/1/1

N2 - Standardized interfaces for efficiently accessing high-throughput sequencing data are a fundamental requirement for large-scale genomic data sharing. We have developed htsget, a protocol for secure, efficient and reliable access to sequencing read and variation data. We demonstrate four independent client and server implementations, and the results of a comprehensive interoperability demonstration. Availability and implementation http://samtools.github.io/hts-specs/htsget.html.

AB - Standardized interfaces for efficiently accessing high-throughput sequencing data are a fundamental requirement for large-scale genomic data sharing. We have developed htsget, a protocol for secure, efficient and reliable access to sequencing read and variation data. We demonstrate four independent client and server implementations, and the results of a comprehensive interoperability demonstration. Availability and implementation http://samtools.github.io/hts-specs/htsget.html.

UR - https://www.scopus.com/pages/publications/85058727946

U2 - 10.1093/bioinformatics/bty492

DO - 10.1093/bioinformatics/bty492

M3 - Article

C2 - 29931085

AN - SCOPUS:85058727946

SN - 1367-4803

VL - 35

SP - 119

EP - 121

JO - Bioinformatics

JF - Bioinformatics

IS - 1

ER -

Htsget: A protocol for securely streaming genomic data

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