What's New in 7.0

The genome portal of the Department of Energy Joint Genome Institute: 2014 updates. Nordberg H, Cantor M, Dusheyko S, Hua S, Poliakov A, Shabalov I, Smirnova T, Grigoriev IV, Dubchak I. Nucleic Acids Res. 2014,42(1):D26-31.

Version 7.0 of the JGI Genome Portal has a few exciting features! If you are new to the portal, you might also want to check out the new features from our previous release here.

Variety of ways to download different data

Available download files are presented in a tree based on the data-type Figure 1. Download function access page for Fusobacteria project. A user can select any relevant data set/s of raw data, genome assembly and analysis results

1. Many new types of JGI data are now available to download (fig.1):

File types supported:

  • All RAW
  • Assemblies
  • Quality Control
  • Results of analysis
  • Files archived to tape (NERSC HPSS)

2. For users who need to download a large number of files or large files (up to several hundred gigabytes), data are available via the public JGI endpoint on Globus (https://www.globus.org).

3. For users who need to download data using scripting or programming we provide the service described in the documentation on the Genome Portal web site.

Expanded powerful genome Search!

screenshot of Search Results Figure 2. Search results table. ‘Info’ link in the Resources column leads to an individual portal of each found data set.

The new release includes powerful new search tools to support the growing volume of sequence data at the JGI. Users can locate and view sequencing projects using GenBank accession number, taxonomic information, Principal Investigator contact, and many other search terms.(fig.2)

Community Science Program JGI Proposals, that include multiple genomes, transcriptomes, or other data sets, now have "group" portals aggregating individual portals within the proposal and providing a single access point for download of all data related to the proposal.

Data Organization and access

screenshot of search Figure 3. Individual portal page for the Wetland Surface Sediment Metagenome project. Relevant information is classified into several sections including ‘Groups’ that specifies an appropriate proposal or large-scale JGI programs.

Individual Genome Portal project sites ‘portals’ (fig.3) give access to each project data and relevant analytical tools. More than 15 000 DOE JGI projects of different types (standard and improved draft, finished genomes, gene expression profiling, resequencing, metagenome projects, single cell projects, transcriptomes, metatranscriptomes, exomes, and others) are publicly available.

The Genome Portal also provides access to over 17 000 annotated genomes and metagenomes, along with specialized analytical tools to navigate these data sets and compare genomes.