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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

10 datasets

Data from: Tripal EUtils - A Tripal module to increase exchange and reuse of genome assembly metadata

Genomics
    A core component of NCBI’s BioSample metadata are the BioSample “packages” ([https://www.ncbi.nlm.nih.gov/biosample/docs/packages/](https://www.ncbi.nlm.nih.gov/biosample/docs/packages/)). Data submitters can choose a package, which contain a variety of attribute sets, such as plant- or insect-specific attributes, attribute values as recommended by the MIxS standard, etc. Here, we provide suggested ontology term mappings for attributes from the Invertebrate 1.0 and Plant 1.0 packages. This dataset corresponds to Table 4 in the corresponding publication in the journal Database.

    Cimex Lectularius Genome Assembly 1.0

      The Baylor College of Medicine recently sequenced and annotated the Cimex lectularius genome as part of the i5k pilot project. The C. lectularius research community has manually reviewed and curated the computational gene predictions and generated an official gene set, OGSv1.2. This dataset presents the Cimex lectularius 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.

      Onthophagus taurus Genome Annotations v0.5.3

        The Baylor College of Medicine recently sequenced and annotated the Onthophagus taurus genome as part of the i5k pilot project. NOTE: This gene set is an unstable pre-release (v0.5.3), and was provided to facilitate manual curation and analyses before the official gene set is released. Gene identifiers from this gene set will likely not be maintained.

        Onthophagus taurus Genome Assembly 1.0

          The Baylor College of Medicine recently sequenced and annotated the Onthophagus taurus genome as part of the i5k pilot project. This dataset presents the Onthophagus taurus 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.

          Hyalella azteca Official Gene Set v1.0

            The Hyalella azteca genome was recently sequenced and annotated as part of the i5k pilot project by the Baylor College of Medicine. The Hyalella azteca research community has manually reviewed and curated the computational gene predictions and generated an official gene set, OGSv1.0. The OGS is an integration of automatic gene predictions from Maker with manual annotations by the research community (via the Apollo manual annotation software).

            Blattella germanica Official Gene Set OGSv1.0

              The *Blattella germanica* genome was recently sequenced and annotated as part of the i5k pilot project by the Baylor College of Medicine. The *Blattella germanica* research community has manually reviewed and curated the computational gene predictions and generated an official gene set, OGSv1.0.

              Anoplophora glabripennis Official Gene Set OGSv1.2

                The *Anoplophora glabripennis* genome was recently sequenced, assembled and annotated as part of the i5k pilot project by the Baylor College of Medicine, in collaboration with the McKenna Laboratory at the University of Memphis. The *Anoplophora glabripennis* research community has manually reviewed and curated the computational gene predictions and generated an official gene set, OGSv1.2. OGSv1.2 was generated by merging gene set AGLA-c0.5.3-Models generated by the Baylor College of Medicine, and community-curated models in the Apollo software, after QC of the Apollo output.

                Anoplophora glabripennis genome annotations v0.5.3

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