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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

114 datasets

Halyomorpha halys Official Gene Set v1.2

    This dataset presents the Halyomorpha halys Official Gene Set (OGS) v1.2. OGSv1.2 and is an update of Halyomorpha halys OGSv1.1 (https://doi.org/10.15482/USDA.ADC/1504240) to the coordinates of genome assembly GCA_000696795.3 (https://www.ncbi.nlm.nih.gov/assembly/GCA_000696795.3) using https://github.com/NAL-i5K/coordinates_conversion/.

    Halyomorpha halys Official Gene Sets v1.0 and v1.1

      This dataset presents the *Halyomorpha halys* Official Gene Set (OGS) v1.0 and v1.1. The OGS is an integration of automatic gene predictions from NCBI's eukaryotic annotation pipeline, [NCBI Halyomorpha halys Annotation Release 100](https://www.ncbi.nlm.nih.gov/genome/annotation_euk/Halyomorpha_halys/100/), with manual annotations by the research community (performed via the Apollo manual curation software, http://genomearchitect.org/).

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

        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.

        Drosophila eugracilis genome annotations v0.5.3 for genome assembly Deug05112011

          This research on Drosophila eugracilis genomics is part of the Drosophila modENCODE project.The Baylor College of Medicine is studying the comparative genomics of eight species of Drosophila, including biarmipes, bipectinata, elegans, eugracillis, ficusphila, kikkawai, rhopaloa, and takahashii. RNA-Seq data were used with additional protein homology data for a MAKER automated annotation of the Drosophila eugracilis genome assembly Deug05112011. This gene set is an unstable pre-release (v0.5.3), and is provided to facilitate manual curation and analyses. Gene identifiers from this gene set will not be maintained.

          Drosophila ficusphila genome annotations v0.5.3 for genome assembly Dfic02082011

            This research on Drosophila ficusphila genomics is part of the Drosophila modENCODE project.The Baylor College of Medicine is studying the comparative genomics of eight species of Drosophila, including biarmipes, bipectinata, elegans, eugracillis, ficusphila, kikkawai, rhopaloa, and takahashii. RNA-Seq data were used with additional protein homology data for a MAKER automated annotation of the Drosophila ficusphila genome assembly Dfic02082011. This gene set is an unstable pre-release (v0.5.3), and is provided to facilitate manual curation and analyses. Gene identifiers from this gene set will not be maintained.