a gif of people moving through a hallway at the JGI

Vision 

Lead genomic innovation for a sustainable bioeconomy.

Mission 

As a U.S. Department of Energy Office of Science user facility, we provide advanced genomic capabilities, large-scale data, and professional expertise to support the global research community in studies of complex biological and environmental systems. We optimize our service to the community through responsibly managing our people and resources.

 

Director's Perspective

 

Honors & Awards

  • An image of four individuals, one holding a trophy, honors Yasuo Yoshikuni for receiving the 10th Yamamotto Scientific Award
  • A slide includes a headshot and honors Nikos Kyrpides receiving the 2022 Scientific Career award.
  • Six headshots honor Igor Grigoriev, Natalia Ivanova, Nikos Kyrpides, Dan Rokhsar, Simon Roux, Jeremy Schmutz, Susannah Tringe and Tanja Woyke for being named Highly Cited Researchers by Clarivate.

Accomplishments at a Glance

Below are briefs on some of the scientific collaborations that came out of the JGI in 2023, as well as highlights around our outreach efforts.
Science Feature
A Collaboration to Improve Plant Genome Annotations Across Species
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DOE Science Highlights
Sequencing Sphagnum Leads to Discovery of Sex Chromosomes
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DOE Science Highlights
Eelgrass Proves to Be Much Younger Than We Thought
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DOE Science Highlights
Busting the Unbreakable Lignin
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DOE Science Highlights
Tracing the Evolution of Shiitake Mushrooms
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DOE Science Highlights
Supercharging SIP in the Fungal Hyphosphere
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DOE Science Highlights
New Research Sheds Light on Diversity in the Deep Sea
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DOE Science Highlights
You Can Move, But You Can’t Hide
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DOE Science Highlights
iPHoP: A Matchmaker for Phages and their Hosts
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DOE Science Highlights
For the Tiniest Archaea, A Genomic Switch of Friend or Foe
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DOE Science Highlights
New Research Finds Flagella in the Terrestrial Roots of Marine Bacteria
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Science Feature
From Berkeley to Binghamton: Tracking Strawberry Evolution
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Impact: By the Numbers

Spending Profile

Animated gif shows spending profile by percentage of total budget: genomic technologies—34.7%; science programs and analysis—32.2%; data science and informatics—15%; management—7.5%; project management office—3.8%; compute infrastruture & support team (@NERSC)—4.2%; operations—2.6%

Users on the Global Map

An animated map of the world shows how users are distributed globally: North America—1,694 (U.S.—1,592); South America—34; Europe—479; Africa—14; Asia—82; Australia/New Zealand—70. A chart in the corner shows distribution by type of user: Academic—1,708; Industry—38; DOE nat'l labs—208; Government—235; Other—184; Total Users—2,373
RegionCountRegionCountRegionCountRegionCount
North America1,694Asia82Europe479  
United States1,592China24Austria13Norway18
Canada95India10Belgium17Poland2
Mexico7Israel9Croatia1Portugal7
  Japan29Czech Republic13Russia5
South America34Malaysia1Denmark17Serbia2
Argentina1Singapore3Estonia2Slovenia2
Brazil23South Korea6Finland13Spain43
Chile2  France62Sweden28
Colombia1Africa14Germany86Switzerland12
Ecuador1Morocco1Greece10Turkey1
Peru1South Africa12Hungary10United Kingdom60
Uruguay5Tunisia1Iceland1  
    Ireland3Australia + New Zealand70
    Italy22Australia53
    Netherlands29New Zealand17

Users on the U.S. Map

A map of the U.S. shows a breakdown of users in the country: (354) California; (30–74) Wisconsin, Michigan, Washington, Colorado, New York, Georgia, Illinois, Massachusetts, Tennessee, Ohio, Arizona, Missouri, North Carolina, Florida, Minnesota, Montana, Texas; (11–29) Oregon, New Mexico, Connecticut, Alabama, Indiana, Maryland, Nebraska, New Jersey, Delaware, New Hampshire, Pennsylvania, Utah, Hawaii, Iowa, Virginia ; (0–10) Kansas, Oklahoma, South Carolina, Louisiana, West Virginia, Maine, Nevada, Rhode Island, Arkansas, Idaho, Missouri, North Dakota, Washington D.C., Puerto Rico, Vermont, Kentucky, Wyoming, Alaska, South Dakota. A box in the corner shows a breakdown by industry: Academic—1,190; Industry—28; DOE nat'l labs—208; Government—76; Other—90; Total Users—1,592

Cumulative Number of Projects Completed

Cumulative Number of Scientific Publications

A side-by-side graphic shows projects completed and publications over the last 10 years. Projects: 2014-11,770; 2015-16,313; 2016-23,047; 2017-31,476; 2018-38,999; 2019-82,539; 2020-104,988; 2021-142,076; 2022-179,990; 2023-219,860. Publications: 2014-1,207; 2015-1,388; 2016-1,555; 2017-1,702; 2018-1,934; 2019-2,156; 2020-2,368; 2021-2,610; 2022-2,862; 2023-3,100.

Sequencing Output 

(in billions of bases or GB)

The JGI supports short- and long-read sequencers, where a read refers to a sequence of DNA bases. Short-read sequencers produce billions of paired-end 150 basepair reads used for quantification, such as in gene expression analysis. Long-read sequencers currently average 60,000–70,000 bp reads and are used for de novo genome assembly. Combined short-read and long-read totals per year give JGI’s annual sequence output. The total sequence output in 2023 was 716,929 GB.

chart in billions of basepairs

 Users Letters of Intent/Proposals Submitted & Approved

A bar graph showing letters of intent received and approved, as well as proposals submitted and approved, for proposal calls. Community Science Program: (2022) LOIs submitted-50; LOIs approved-46; Proposals submitted-41; Proposals approved-17. (2023) LOIs submitted-46; LOIs approved-39; proposals submitted-35; proposals approved-19. FICUS(JGI-EMSL): (2022)LOIs submitted-56; LOIs approved-54; proposals submitted-52; proposals approved-11. (2023) LOIs submitted-47; LOIs approved-45; proposals submitted-43; proposals approved-10. New Investigator: (2022) proposals submitted-55; proposals approved-20. (2023) proposals submitted-64; proposals approved-26. Functional Genomics: (2022) proposals submitted-24; proposals approved-10. (2023) proposals submitted-19; proposals approved-9.

Computational Infrastructure: Users of JGI Tools & Data

The Genome Portal provides unified access to all JGI genomic databases and analytical tools. Users can search, download and explore data sets available for all JGI sequencing projects including their status, assemblies, and annotations of sequenced genomes. The Data Portal allows JGI users to more easily access public data sets through a common set of metadata across files submitted by each scientific program. The Genome Portal will be retired once the Data Portal reaches data- and feature-parity with its predecessor. FY2023 improvements to the Data Portal include improved data parity, cart download, navigation by pagination, and significant progress on privileged access and access management.

  • JGI Archive and Metadata Organizer (JAMO): 15.192 million file records
  • JAMO Archived Data Footprint: 15.952 Petabytes
  • Data Downloads in FY23:
    • Genome Portal: 7.286 million file-downloads
    • Data Portal: 0.633 million file-downloads
    • Total: 7.919 million file-downloads

Since the retirement of NERSC’s Cori system, a number of JGI’s pipelines and processes have moved out of NERSC to the JGI’s new informatics cluster, Dori, situated at LBL’s LabIT, and the computing infrastructure at IGB. This has required JGI’s data management system, JAMO (JGI Archive and Metadata Organizer), to expand operations across data centers — both ingesting new data and delivering data stored at NERSC for processes running at these other centers. This has been our first step in creating a distributed version of JAMO, which in the future will be capable of sharing data across registered lab members. 

As part of our business continuity planning, JGI has worked with the Environmental Molecular Sciences Laboratory to enable JAMO to automatically transmit and store files on EMSL’s HPSS tape system via Globus. Currently, all new raw sequencing data is being transmitted. Over the next year, all legacy data will be restored from NERSC’s tape system and transmitted automatically to EMSL.

Computational graphic by Neil Byers, JGI.  Photography and cinemagraphs by Thor Swift, Berkeley Lab. ‘By the Numbers’ infographics by Creative Services, IT Division, Berkeley Lab.

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