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

Cyber Resilience and Intelligence Divisi

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

18 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].

Funders	Funder number
Wellcome Trust	201535/ Z/16/Z, 100956/Z/13/Z

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10.1093/bioinformatics/bty492

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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

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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",

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doi = "10.1093/bioinformatics/bty492",

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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

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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

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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.

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DO - 10.1093/bioinformatics/bty492

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Htsget: A protocol for securely streaming genomic data

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