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Ag Data Commons migration begins October 18, 2023

The Ag Data Commons is migrating to a new platform – an institutional portal on Figshare. Starting October 18 the current system will be available for search and download only. Submissions will resume after the launch of our portal on Figshare in November. Stay tuned for details!

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

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).

    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).

      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.

        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.

          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.

            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.

              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/)).