htsget

Allows users to download read and variation data for subsections of the genome

Overview

Summary Benefits Target users Announcements

With great advances in sequencing technologies, research and healthcare settings are generating more data than ever before. The ability to share and access these large volumes of data to enable new scientific discoveries, however, remains a challenge. Today, this is largely achieved by transferring and copying large files between two computers, resulting in a slow and resource-intensive process that is unscalable. The htsget API enables faster retrieval of read and variation data by allowing users to download subsections of the genome in which they are interested.

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htsget

Benefits

Allows users to download only parts of a genome of interest
Enables faster and more efficient access to data

Target users

Researchers

Announcements

Date	Title
29 January 2026	New GA4GH implementation story: Rakeiora Genomics Platform in New Zealand

Title	Related Driver Projects and Organisations
All of Us Researcher Workbench	All of Us Research Program
Australian Genomics Data Management Systems	Australian Genomics
CanDIG V2	Canadian Distributed Infrastructure for Genomics (CanDIG)
EJP-RD Virtual Platform	European Joint Programme on Rare Disease (EJP RD)
ELIXIR European Genome-phenome Archive (EGA)	European Genome-phenome Archive (EGA)
ELIXIR-Beacon	ELIXIR Beacon
Federated EGA	European Genome-phenome Archive (EGA), EMBL's European Bioinformatics Institute (EBI), Centre for Genomic Regulation
Genomics England Research Environment	Genomics England
National Genomic Information System (NGIS)	Genomics England

Share your implementation

Publications Documents Videos

Publications

Title	Author(s)	Year
Rakeiora Genomics Platform: a pathfinder for genomic medicine research in Aotearoa New Zealand	Rye, C.E. et al. Rye, C.E., Puketapu-Watson, H., Wihongi, H., Te Aika, B., de Ligt, J., Print, C.G., Tsai, P., Curran, B., Jones, N., Huh, J, Owen Perkins, E., Pestle, M., Zhao, K., Halytskyy, Y., Robertson, S.P., Halliday, B.J., Goodin, E., Markie, D.M., Lamont, A., Wilcox, P.	2025
Remote visualization of large-scale genomic alignments for collaborative clinical research and diagnosis of rare diseases	Corvò, A. et al. Corvò, A., Matalonga, L., Spalding, D., Senf, A., Laurie, S., Picó-Amador, D., Paramonov, I., Foix Romero, A., Garcia-Rios, E., Izquierdo Ciges, J,, Mohan, A., Thomas, C., Halmagyi, C., Freeberg, M.A., Töpf, A., Horvath, R., Saunders, G., Gut, I., Keane, T., Piscia, D., Beltran, S.	2020
Htsget: A protocol for securely streaming genomic data	Kelleher, J. et al. 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.	2018

Documents

Date	Title
14 September 2023	Code of Ethics and Community Conduct (CECC)
11 March 2023	Meeting minutes: Htsget
12 December 2020	Meeting minutes: LSG — htsget (2021 to 2022)

Videos

	Date	Title
	5 December 2018	Using the GA4GH toolkit: htsget streaming API for genomic data

Contributors Driver Projects

Contributors

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John Marshallhtsget LeadCentre for Population Genomics
Jeremy AdamsOntario Institute for Cancer Research (OICR), Toronto, Canada
Edmon BegoliOak Ridge National Laboratory (ORNL), Oak Ridge
Robert DaviesWellcome Sanger Institute (WSI), Hinxton, UK
Mallory FreebergEMBL's European Bioinformatics Institute (EBI), Hinxton, UK
David GlazerVerily, South San Francisco, CA, USA
Oliver HofmannUniversity of Melbourne Centre for Cancer Research, Melbourne
David JacksonWellcome Sanger Institute (WSI), Hinxton, UK
Jerome KelleherUniversity of Oxford, Oxford
Anders LeungIndependent Contributor
Mike LinIndependent Contributor
Yash PuligundlaBroad Institute of MIT and Harvard, Cambridge, US
Shaikh Farhan RashidUniversity Health Network, Toronto, Canada, Canadian Distributed Infrastructure for Genomics (CanDIG)
Augusto RendonGenomics England
Roman Valls GuimeraUniversity of Melbourne Centre for Cancer Research, Melbourne

Driver Projects

Title	Thematic Area
All of Us Research Program	Rare Disease Cancer Complex Traits
Australian Genomics	Rare Disease Cancer Complex Traits
CHU Sainte-Justine Research Center
European Joint Programme on Rare Disease (EJP RD)	Rare Disease
European Genome-phenome Archive (EGA)	Rare Disease Cancer Complex Traits Basic Biology
Genomics England	Rare Disease Cancer Complex Traits

Version history

Version	Maintenance	Development	PDAP Review	Date
htsget v1.3	Maintained	Development	Draft	24 May 2022
htsget v1.2	Maintained	Development	Draft	13 May 2019
htsget v1.1.1	Maintained	Development	Draft	23 Jan 2019
htsget v1.1	Maintained	Development	Draft	1 Jun 2018
htsget v1.0	Maintained	Development	Draft	10 Oct 2017