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Ag Data Commons migration begins October 18, 2023

The Ag Data Commons is migrating to a new platform – an institutional portal on Figshare. Starting October 18 the current system will be available for search and download only. Submissions will resume after the launch of our portal on Figshare in November. Stay tuned for details!

i5k Workspace

About the i5k Workspace@NAL

The i5k Workspace (https://i5k.nal.usda.gov) is an inclusive genome portal for any arthropod genome project that would like to make use of our resources. We provide download services, BLAST, the JBrowse genome browser, and the Apollo manual curation service. Over 50 arthropod genomes are now part of the i5k Workspace, and users are encouraged to browse the genomes that we host, and contribute to the curation of each genome. For more information about the i5k Workspace, you can read our paper on the i5k Workspace, view our posters and talks, and find our software projects on github. The Ag Data Commons is now hosting a growing number of i5k Workspace datasets.

About the i5k initiative

The i5k initiative is a transformative project that aims to sequence and analyze the genomes of 5,000 arthropod species. The National Agricultural Library has partnered with the i5k initiative to create the i5k Workspace@NAL, which serves any ‘orphaned’ arthropod genome project's hosting needs. For more information about the i5k initiative, read the paper and visit the website.

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i5k Datasets

114 datasets

Ephemera danica Official Gene Set ephdan_OGSv1.0

    This dataset presents the *Ephemera danica* Official Gene Set (OGS) v1.0. The OGS is an integration of automatic gene predictions from *Ephemera danica* genome annotations v0.5.3, with manual annotations by the research community. Manual and automated annotations were lifted over from genome assembly *Ephemera danica* genome assembly v1.0 to genome assembly Edan_2.0 using the coordinates_conversion and remap-gff3 programs.

    Leptinotarsa decemlineata genome assembly 1.0

      This dataset presents the Leptinotarsa decemlineata genome v1.0. This assembly version is the pre-release version, prior to filtering and quality control by the [National Center for Biotechnology Information's GenBank resource](http://www.ncbi.nlm.nih.gov/assembly/GCA_000696205.1)

      Oncopeltus fasciatus genome assembly 1.0

        The Baylor College of Medicine recently sequenced and annotated the Oncopeltus fasciatus genome as part of the i5k pilot project. The O. fasciatus research community has manually reviewed and curated the computational gene predictions and generated an official gene set, OGSv1.1. This dataset presents the Oncopeltus fasciatus genome v1.0. This assembly version is the pre-release version, prior to filtering and quality control by the National Center for Biotechnology Information's GenBank resource.

        Orussus abietinus Official Gene Set OGSv1.0

          The Orussus abietinus genome was recently sequenced and annotated as part of the i5k pilot project by the Baylor College of Medicine. The Orussus abietinus research community has manually reviewed and curated the computational gene predictions and generated an official gene set, OGSv1.0. The general procedure for generating this OGS is outlined here: https://github.com/NAL-i5K/I5KNAL_OGS/wiki. OGSv1.0 was generated by merging gene set OABI-V0.5.3-Models generated by the Baylor College of Medicine, and community-curated models in the Apollo software, after QC of the Apollo output.

          Athalia rosae Official Gene Set OGSv1.0

            The Athalia rosae genome was recently sequenced and annotated as part of the i5k pilot project by the Baylor College of Medicine. The Athalia rosae research community has manually reviewed and curated the computational gene predictions and generated an official gene set, OGSv1.0. The general procedure for generating this OGS is outlined here: https://github.com/NAL-i5K/I5KNAL_OGS/wiki. OGSv1.0 was generated by merging gene set AROS-V0.5.3-Models generated by the Baylor College of Medicine, and community-curated models in the Apollo software, after QC of the Apollo output.

            Orussus abietinus genome annotations v0.5.3

              This dataset presents the Orussus abietinus gene set BCM_v_0.5.3. RNA-Seq data was used with additional protein homology data for a MAKER automated annotation of the Orussus abietinus genome assembly 1.0.

              Athalia rosae genome annotations v0.5.3

                This dataset presents the Athalia rosae gene set BCM_v_0.5.3. RNA-Seq data was used with additional protein homology data for a MAKER automated annotation of the Athalia rosae genome assembly 1.0.

                Halyomorpha halys genome assembly v1.0

                  The Baylor College of Medicine has sequenced and annotated the Halyomorpha halys genome as part of the i5k pilot project. This dataset presents the Halyomorpha halys genome v1.0. This assembly version is the pre-release version, prior to filtering and quality control by the National Center for Biotechnology Information's GenBank resource. If you wish to use this dataset, please follow the Baylor College of Medicine's conditions for data use: https://www.hgsc.bcm.edu/bcm-hgsc-conditions-use

                  Halyomorpha halys genome annotations v0.5.3

                    This dataset presents the Halyomorpha halys gene set BCM_v_0.5.3. RNA-Seq data was used with additional protein homology data for a MAKER automated annotation of the Halyomorpha halys genome assembly 1.0. If you wish to use this dataset, please follow the Baylor College of Medicine's conditions for data use: https://www.hgsc.bcm.edu/bcm-hgsc-conditions-use

                    Frankliniella occidentalis genome annotations v0.5.3

                      This dataset presents the Frankliniella occidentalis gene set BCM_v_0.5.3. RNA-Seq data was used with additional protein homology data for a MAKER automated annotation of the Frankliniella occidentalis genome assembly 1.0.