Genome Projects Help

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The Genome Projects page allows you to search for JGI sequencing projects and retrieve data about all projects that meet your search criteria. When the page first loads, the filters are set to show all projects in the database. You can refine the list of projects to show only the subset in which you're interested by entering search text or selecting options from the menus.

Searching for Text
Filtering by Program and Year
Filtering by Taxon
Reported Fields
Bookmarking a Search

Searching for Text

You can enter text to search for any project with that text in its project tracking data. You can also narrow the search to find only projects with your search text in a specific field. To search all text, leave the Show Projects menu set to "any text". To search a specific field, select "taxonomic name", "common name", "PI name", "proposal ID", "project ID", or "NCBI taxonomy ID" from the Show Projects menu.

The search is case insensitive. A search for "geo" returns "Geobacter" and "Biogeochemically important bacteria".

Any project that contains the text you entered in the field(s) you selected will be returned. If you enter more than one word, the text you entered is treated as a phrase. A search for "geobacter sp. strain sz" returns "Geobacter sp. strain SZ" but not "Geobacter sp. M18".

You can use an asterisk (*) as a wildcard in your search string. The search will return results with zero or more characters in the position of the asterisk. A search for "geobacter*ens" returns "Geobacter sulfurreducens" as well as "Geobacter metallireducens"

If you are searching within a numeric field (project ID, proposal ID, or NCBI taxonomy ID), search text wih alphabetic characters will not return any results.

Filtering by Program and Year

To view projects in a specific JGI sequencing program or year, select the program name or year in the Show Projects From filter. To view only projects from a specific program that were accepted for sequencing in a particular year, select the program from the first menu and the year from the second menu.

CSP: Community Sequencing Program

DOEM: DOE Microbial Genome Program

GEBA: Genomic Encyclopedia of Bacteria and Archaea

GTL: DOE Genomics: GTL Program

LSP: Laboratory Science Program

Filtering by Taxon

To view all sequencing projects of a particular superkingdom, select that taxon from the Show Projects of Taxon menu. This menu also includes options to view only organelle or metagenome projects.

Reported Fields

Name: The name of the project in JGI's project tracking system.

Scope: The scope of work planned for the project. WGS indicates whole-genome shotgun sequencing. SCS indicates single-clone shotgun sequencing.

Taxon: The superkingdom of the organism to be sequenced. Since metagenomes by nature can include a unknown assortment of organisms, no superkingdom is given for metagenomes.

Status: The current state of progress on the sequencing project. Sequencing statuses reflect a phase of sequencing, listed first, and a more precise status within that phase. Click the link to view more detailed status information. Not all projects go through all the same steps.

Awaiting Material: We are waiting for DNA or the DNA is waiting to enter the production process.
Library: The project is in Sample QC (a check of the quality of the sample submitted) or Library Construction (building the libraries to be sequenced).
Production: This phase begins with a Library QC step to make sure the libraries are ready for production sequencing. Checkpoint Sequencing is conducted until enough sequence has been obtained for a Checkpoint Assembly—a brief stop in the Assembly phase before Final Sequencing.
Assembly: The project is either actively being assembled or awaiting assembly.
Post-Draft Sequencing: This is postproduction work (such as Finishing or Genome Improvement) that is not conducted for all genomes.
Complete: The project has been released. Some are released as a Permanent Draft (some gaps remain in the sequence that we do not plan to close), some go into Genome Improvement (e.g., closing gaps, increasing scaffold sizes in a draft genome), and others are released as Finished genomes (usually all gaps are closed and all base pairs meet specific quality criteria).
Abandoned: We have chosen not to continue sequencing the organism. An abandoned organism is typically replaced by another organism that will better satisfy the needs of the proposal.

Tools: Online resources for analyzing or obtaining sequence from this project. For projects that have not yet been released, no tools are available. Click a tool link to go directly to that tool's data for the project.

Program: The JGI sequencing program and year for which the project was accepted.

Propsal: Many proposals involve multiple projects at JGI. The proposal identifies the initial request for sequencing from the collaborator. If a link appears, click it to view information and a rationale for the proposal.

Contact: The principal investigator for the project is shown, as is the project manager. Click a link from a contact name to initiate an email to the contact.

Last Updated: The date on which data for the project was last updated in the JGI project tracking system.

Bookmarking a Search

If you find a particular filter setting that you would like to return to in the future, you may want to save a bookmark for it. Before using your browser's bookmark feature, be sure to click the Go button. This forces the page to reload and update the location field in your browser. (As you make changes to the filter settings, the data updates without a page reload. This makes searches faster, but it means that the location field in your browser will not update for each search unless you click the Go button.)