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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

110 datasets

Frankliniella occidentalis Official Gene Set OGSv1.0

    The *Frankliniella occidentalis* genome was recently sequenced and annotated as part of the i5k pilot project by the Baylor College of Medicine. The *Frankliniella occidentalis* research community has manually reviewed and curated the computational gene predictions and generated an official gene set, OGSv1.0. OGSv1.0 was generated by merging gene set FOCC-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. After the merge, scaffolds that were likely bacterial contamination were identified by John H. Werren, and gene models overlapping with these contaminated regions were removed from the OGS.

    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.

        Drosophila ficusphila 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. The genome assembly presented here is the pre-submission version of Dfic_2.0, which is archived at the National Center for Biotechnology as GCA_000220665.2.

          Drosophila eugracilis 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. The genome assembly presented here is the pre-submission version of Deug_2.0, which is archived at the National Center for Biotechnology as GCA_000236325.2.

            Drosophila rhopaloa genome annotations v0.5.3 for genome assembly Drho05162011

              This research on Drosophila rhopaloa 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 rhopaloa genome assembly Drho05162011. 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 rhopaloa genome assembly Drho05162011

                This research on Drosophila rhopaloa 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. The genome assembly presented here is the pre-submission version of Drho_2.0, which is archived at the National Center for Biotechnology as GCA_000236305.2.

                Drosophila kikkawai genome annotations v0.5.3 for genome assembly Dkik02082011

                  This research on Drosophila kikkawai 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 kikkawai genome assembly Dkik02082011. 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 kikkawai genome assembly Dkik02082011

                    This research on Drosophila kikkawai 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. The genome assembly presented here is the pre-submission version of Dkik_2.0, which is archived at the National Center for Biotechnology as GCA_000224215.2.