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    Designer DNA: JGI Helps Users Blaze New Biosynthetic Pathways
    In a special issue of the journal Synthetic Biology, JGI scientific users share how they’ve worked with the JGI DNA Synthesis Science Program and what they’ve discovered through their collaborations.

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    A genetic element that generates targeted mutations, called diversity-generating retroelements (DGRs), are found in viruses, as well as bacteria and archaea. Most DGRs found in viruses appear to be in their tail fibers. These tail fibers – signified in the cartoon by the blue virus’ downward pointing ‘arms’— allow the virus to attach to one cell type (red), but not the other (purple). DGRs mutate these ‘arms,’ giving the virus opportunities to switch to different prey, like the purple cell. (Courtesy of Blair Paul)
    A Natural Mechanism Can Turbocharge Viral Evolution
    A team has discovered that diversity generating retroelements (DGRs) are not only widespread, but also surprisingly active. In viruses, DGRs appear to generate diversity quickly, allowing these viruses to target new microbial prey.

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    Algae growing in a bioreactor. (Dennis Schroeder, NREL)
    Refining the Process of Identifying Algae Biotechnology Candidates
    Researchers combined expertise at the National Labs to screen, characterize, sequence and then analyze the genomes and multi-omics datasets for algae that can be used for large-scale production of biofuels and bioproducts.

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    This data image shows the monthly average sea surface temperature for May 2015. Between 2013 and 2016, a large mass of unusually warm ocean water--nicknamed the blob--dominated the North Pacific, indicated here by red, pink, and yellow colors signifying temperatures as much as three degrees Celsius (five degrees Fahrenheit) higher than average. Data are from the NASA Multi-scale Ultra-high Resolution Sea Surface Temperature (MUR SST) Analysis product. (Courtesy NASA Physical Oceanography Distributed Active Archive Center)
    When “The Blob” Made It Hotter Under the Water
    Researchers tracked the impact of a large-scale heatwave event in the ocean known as “The Blob” as part of an approved proposal through the Community Science Program.

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    A plantation of poplar trees. (David Gilbert)
    Genome Insider podcast: THE Bioenergy Tree
    The US Department of Energy’s favorite tree is poplar. In this episode, hear from ORNL scientists who have uncovered remarkable genetic secrets that bring us closer to making poplar an economical and sustainable source of energy and materials.

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    Ian Rambo, graduate student at UT-Austin, was a DOE Graduate Student Research Fellow at the JGI
    Virus-Microbe Interactions of Mud Island Mangroves
    Through the DOE Office of Science Graduate Student Research (SCGSR) program, Ian Rambo worked on part of his dissertation at the JGI. The chapter focuses on how viruses influence carbon cycling in coastal mangroves.

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    HPCwire Editor's Choice Award (logo crop) for Best Use of HPC in the Life Sciences
    JGI Part of Berkeley Lab Team Awarded Best Use of HPC in Life Sciences
    The HPCwire Editors Choice Award for Best Use of HPC in Life Sciences went to the Berkeley Lab team comprised of JGI and ExaBiome Project team, supported by the DOE Exascale Computing Project for MetaHipMer, an end-to-end genome assembler that supports “an unprecedented assembly of environmental microbiomes.”

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    With a common set of "baseline metadata," JGI users can more easily access public data sets. (Steve Wilson)
    A User-Centered Approach to Accessing JGI Data
    Reflecting a structural shift in data access, the JGI Data Portal offers a way for users to more easily access public data sets through a common set of metadata.

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    Phytozome portal collage
    A More Intuitive Phytozome Interface
    Phytozome v13 now hosts upwards of 250 plant genomes and provides users with the genome browsers, gene pages, search, BLAST and BioMart data warehouse interfaces they have come to rely on, with a more intuitive interface.

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    screencap from Amundson and Wilkins subsurface microbiome video
    Digging into Microbial Ecosystems Deep Underground
    JGI users and microbiome researchers at Colorado State University have many questions about the microbial communities deep underground, including the role viral infection may play in other natural ecosystems.

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    Yeast strains engineered for the biochemical conversion of glucose to value-added products are limited in chemical output due to growth and viability constraints. Cell extracts provide an alternative format for chemical synthesis in the absence of cell growth by isolating the soluble components of lysed cells. By separating the production of enzymes (during growth) and the biochemical production process (in cell-free reactions), this framework enables biosynthesis of diverse chemical products at volumetric productivities greater than the source strains. (Blake Rasor)
    Boosting Small Molecule Production in Super “Soup”
    Researchers supported through the Emerging Technologies Opportunity Program describe a two-pronged approach that starts with engineered yeast cells but then moves out of the cell structure into a cell-free system.

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    These bright green spots are fluorescently labelled bacteria from soil collected from the surface of plant roots. For reference, the scale bar at bottom right is 10 micrometers long. (Rhona Stuart)
    A Powerful Technique to Study Microbes, Now Easier
    In JGI's Genome Insider podcast: LLNL biologist Jennifer Pett-Ridge collaborated with JGI scientists through the Emerging Technologies Opportunity Program to semi-automate experiments that measure microbial activity in soil.

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    In their approved proposal, Frederick Colwell of Oregon State University and colleagues are interested in the microbial communities that live on Alaska’s glacially dominated Copper River Delta. They’re looking at how the microbes in these high latitude wetlands, such as the Copper River Delta wetland pond shown here, cycle carbon. (Courtesy of Rick Colwell)
    Monitoring Inter-Organism Interactions Within Ecosystems
    Many of the proposals approved through JGI's annual Community Science Program call focus on harnessing genomics to developing sustainable resources for biofuels and bioproducts.

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    Coloring the water, the algae Phaeocystis blooms off the side of the sampling vessel, Polarstern, in the temperate region of the North Atlantic. (Katrin Schmidt)
    Climate Change Threatens Base of Polar Oceans’ Bountiful Food Webs
    As warm-adapted microbes edge polewards, they’d oust resident tiny algae. It's a trend that threatens to destabilize the delicate marine food web and change the oceans as we know them.

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    Integrating JGI Capabilities for Exploring Earth’s Secondary Metabolome
    Natural Prodcast podcast: Nigel Mouncey
    JGI Director Nigel Mouncey has a vision to build out an integrative genomics approach to looking at the interactions of organisms and environments. He also sees secondary metabolism analysis and research as a driver for novel technologies that can serve all JGI users.

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User Programs
Home › User Programs › Product Offerings

Product Offerings

The JGI has diverse capabilities in DNA and RNA sequencing, sample and library preparation, DNA synthesis and pathway engineering, and mass spectrometry based metabolomics.  Below is a table of standard sequencing and synthesis products, including a description of the product and deliverables as well as target cycle times from sample receipt to completion of standard analysis.  (Note: raw data is provided for all products below.  In addition, JGI will submit raw sequence data to SRA once the standard analysis is complete.)

Not all products are available for all proposal calls.  Please review the call language carefully to ensure that your request is appropriate for that call.

Learn more about the average base outputs for each product.

For custom requests not on this list, or to discuss experimental design for a proposal, we encourage you to contact the relevant JGI program leads to discuss available options.

Note: In 2021, we conducted an extensive internal product audit to analyze the scientific value, demand, and costs of current offerings in the JGI product catalog. As a result certain products have been discontinued, including smRNA, bisulfite sequencing, and ChIP-seq.

Scientific Program Product Brief Description Deliverables FY22 target cycle time (median), days* FY22 target cycle time (75th %), days*
DNA Synthesis Constructs <5kb in size Single gene or multiple small genes assembled to less than 5kb in length, cloned into vector of choice Glycerol stock of sequence verified clone 110 110
DNA Synthesis Constructs 5-10kb in size Single gene or multiple small genes assembled totaling 5-10kb in length, cloned into vector of choice Glycerol stock of sequence verified clone 130 130
DNA Synthesis Constructs >10kb in size Gene clusters or pathways totaling more than 10kb in length assembled together, cloned into vector of choice Glycerol stock of sequence verified clone 190 190
DNA Synthesis Combinatorial libraries Multiple genes synthesized and cloned into a vector of choice in various combinations Glycerol stock of sequence verified clones if low number of variants, or pool of variants with sample sequencing to predict the number of successful variants made 230 230
DNA Synthesis Complex libraries Multiple variants of sgRNA or a small coding gene assembled together in various combinations and cloned into a vector of choice; up to 210,000 variants can be made Pool of variant libraries; sample sequencing to determine coverage of variants 230 230
Fungal Minimal Draft Lower coverage short-read whole genome shotgun sequencing Assembly, annotation (Mycocosm) 315 405
Fungal Standard Draft Whole genome shotgun sequencing using long-read sequencing. Exact library types and quality of  finished product depend on genome.  Selected genomes will be improved based on feasibility and scientific merit Assembly, annotation (Mycocosm) 315 405
Fungal Resequencing SNP and short indel calls, rearrangement detection, population analysis Text file of SNPs (incl location in genome, coding/vs non, syn vs non-syn aa change etc) and structural rearrangements, alignment files 300 430
Fungal Transcriptome RNA for expression profiling and genome annotation (single organism). Note: smRNA sequencing is no longer supported. For annotation: de novo assembly.  For counting: text file of gene counts (mapped against reference transcriptome or de novo assembly), alignment files 250 300
Metabolomics Polar metabolite analysis Relative abundance profiling of polar (e.g. amino acids, nucleosides, etc) metabolites using normal phase chromatography coupled to tandem mass spectrometry (detailed description) Metabolite annotation based on chemical standards or computational approaches. Relative abundance of identified metabolites and unidentified features in spectra. based on experimental design based on experimental design
Metabolomics Non-polar metabolite analysis Relative abundance profiling of non-polar (e.g. secondary metabolites, lipids, etc) metabolites using reverse phase chromatography coupled to tandem mass spectrometry (detailed description) Metabolite annotation based on chemical standards or computational approaches. Relative abundance of identified metabolites and unidentified features in spectra. based on experimental design based on experimental design
Metagenome Metatranscriptome

Reference guide

Environmental transcript sequence from prokaryotes and/or eukaryotes Assembly, annotation (IMG/M), mapping to metagenome if applicable 200 215
Metagenome Cell Enrichments
Reference guide
Obtained by physical separation of a biologically relevant unit from a microbial community, such as a microcolony, microbial aggregate, or a specific subset of free-living cells. Due to the low biomass of cell enrichments, the extracted DNA may be amplified using whole-genome amplification prior to sequencing. Assembly, annotation (IMG/M) 200 240
Metagenome Minimal Draft

Reference guide

Lower-coverage short-read assembly & annotation of environmental DNA (note the JGI is no longer supporting iTag sequencing) Assembly, annotation (IMG/M), binning 170 210
Metagenome Standard Draft

Reference guide

Short-read assembly & annotation of environmental DNA.  (Note the JGI is no longer supporting iTag sequencing) Assembly, annotation (IMG/M), binning 170 210
Metagenome Improved Draft

Reference guide

Long-read assembly & annotation of environmental DNA. Assembly, annotation (IMG/M), binning 200 240
Metagenome Stable Isotope Probing (SIP)

Reference guide

Used for the identification of active groups of organisms within a community. Individual samples are fractionated using a density gradient, and a metagenome library is prepared and sequenced for each fraction. individual assembly, combined assembly of related fractions originating from the same sample, annotation (IMG/M), binning depends on project depends on project
Microbial Minimal Draft, Isolate Draft quality microbial assembly of short-read sequence data, many unordered contigs. Assembly, annotation (IMG) 200 270
Microbial Improved Draft, Isolate High quality draft assembly of long-read sequence data, computationally analyzed and improved.  Semi-manual. Assembly, annotation (IMG), methylation analysis 190 330
Microbial Minimal Draft, Single Cell Draft quality microbial assembly of amplified genomes from single cells, many unordered contigs. Assembly, annotation (IMG) 100 120
Microbial Single Particle Sort Draft quality assembly of amplified genomes from sorted cell(s)/particle(s), many unordered contigs. Assembly, annotation (IMG/M) 100 120
Microbial Resequencing SNP and short indel calls, rearrangement detection, population analysis. Text file of SNPs (incl location in genome, coding/vs non, syn vs non-syn aa change etc) and structural rearrangements, alignment files 200 240
Microbial Transcriptome RNA for expression profiling (single organism). Note: smRNA sequencing is no longer supported. For counting: text file of gene counts (mapped against reference transcriptome), alignment files 190 250
Viral Minimal Draft Draft quality viral assembly, many unordered contigs. Assembly, annotation (IMG) 200 270
Viral Single Particle Sort Draft quality assembly of amplified genomes from sorted viral particles, unordered contigs Assembly, annotation (IMG/M) 100 120
Plant and Algal Standard Draft Whole genome shotgun sequencing.  Sequencing generated for initial evaluation varies depending on genome characteristics, availability of external resources and project goals.  Selected genomes will be improved based on feasibility and scientific merit. Assembly, annotation for (Phytozome for plant, Phycocosm for algae) depends on genome depends on genome
Plant and Algal Resequencing SNP and short indel calls, rearrangement detection, population analysis. Text file of SNPs (incl location in genome, coding/vs non, syn vs non-syn aa change etc) and structural rearrangements, alignment files 250 250
Plant and Algal Transcriptome RNA for expression profiling and genome annotation (single organism). Note: smRNA sequencing is no longer supported. For annotation: de novo assembly.  For counting: text file of gene counts (mapped against reference transcriptome or de novo assembly), alignment files 260 360
Plant, Algal, Fungal, and Microbial DAP-seq Used for genome-wide identification of transcription factor binding sites. TF binding sites and motifs project-dependent project-dependent

* Cycle times listed above are based on actual cycle times during FY21.  While we continue to experience some residual COVID-related backlogs, we expect cycle times to decrease during FY22.

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