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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

12 datasets

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).

    i5K Workspace@NAL

      The i5k Workspace @ NAL is a platform for communities around ‘orphaned’ arthropod genome projects to access, visualize, curate and disseminate their data.

      Neodiprion lecontei Official Gene Set v1.1

        This dataset presents the *Neodiprion* Official Gene Set (OGS) v1.1. It was generated using Maker v2.31.8, followed by CrossMap re-mapping of coordinates to genome assembly Nlec1.1 ([https://www.ncbi.nlm.nih.gov/assembly/GCA_001263575.2/](https://www.ncbi.nlm.nih.gov/assembly/GCA_001263575.2/)).

        Oncopeltus fasciatus Official Gene set v1.1

          Oncopeltus fasciatus genome was recently sequenced and annotated as part of the i5k pilot project by the Baylor College of Medicine. 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 Official Gene Set (OGS) v1.1. The OGS is an integration of automatic gene predictions from Maker (done by Dan Hughes at Baylor) with manual annotations by the research community (done via Web Apollo).

          Oncopeltus fasciatus Official Gene set v1.2

            This dataset presents the Oncopeltus fasciatus Official Gene Set (OGS) v1.2. The OGS is an update of OGSv1.1. Manual annotations from the Apollo manual annotation tool were merged with OGSv1.1 using the NAL's [prototype Merge program](https://github.com/NAL-i5K/I5KNAL_OGS).

            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.

              Genes of viral origin in the Fopius arisanus genome

                *Fopius arisanus* (Sonan) is a braconid wasp (subfamily Opiinae) and biological control agent of a broad range of tephritid fruit fly species, including the global pests Mediterranean fruit fly *Ceratitis capitata* and the Oriental fruit fly *Bactrocera dorsalis*. In an effort to create foundational genomic resources for this species, the complete genome and transcriptomes for several wasp life stages have been recently generated. Manual annotation of 55 viral genes and phylogenetic analysis revealed that *F. arisanus* has independently acquired a symbiotic virus related to alpha-nudiviruses.

                Oncopeltus fasciatus genome annotations v0.5.3

                  The Oncopeltus fasciatus genome was recently sequenced and annotated as part of the i5k pilot project by the Baylor College of Medicine. 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 gene set BCM_v_0.5.3, which was generated computationally. RNA-Seq data was used with additional protein homology data for a MAKER automated annotation of the Oncopeltus fasciatus genome assembly 1.0.

                  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.