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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

111 datasets

Manual annotations of Rhyzopertha dominica genome assembly RdoDt3_Drdd8_decomES

    This dataset contains manual annotations from Rhyzopertha dominica community curators, based on genome assembly RdoDt3_Drdd8_decomES.fasta.gz. These annotations are direct exports from Apollo 2.6 (https://doi.org/10.5281/zenodo.5015109), hosted by the i5k Workspace@NAL (https://i5k.nal.usda.gov/). Manual annotations are temporary and will be reviewed by the i5k Workspace@NAL and submitted to NCBI's GenBank database after review.

    Data from: A High-Quality Genome Assembly from a Single, Field-collected Spotted Lanternfly (Lycorma delicatula) using the PacBio Sequel II System

      A 2.3 Gb *de novo* genome assembly of a field-collected adult female Spotted Lanternfly (*Lycorma delicatula*) using a single PacBio SMRT Cell is provided. Supporting files for the manuscript "A High-Quality Genome Assembly from a Single, Field-collected Spotted Lanternfly (*Lycorma delicatula*) using the PacBio Sequel II System", include several intermediate versions of the assembly (raw output from Falcon, raw output from Falcon unzip, etc.) as well as the final assembly primary contigs and haplotigs (for the regions of the genome that were phased).

      Oncopeltus fasciatus hybrid genome assembly 1.0

        The milkweed bug, *Oncopeltus fasciatus*, was sequenced as part of the i5k pilot project from Baylor College of Medicine (Illumina data). To augment those resources, we present here a hybrid genome assembly with low coverage PacBio data, assembled with PBJelly: the *Oncopeltus fasciatus* Hybrid Genome Assembly v1.0.

        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.

          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.