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The Ag Data Commons is migrating

The Ag Data Commons is migrating to a new institutional portal on Figshare. The current system is available for search and download only. The new platform is open for submission with assistance from Ag Data Commons curators. Please contact NAL-ADC-Curator@usda.gov, if you need to publish or update your datasets.

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

94 datasets

Gerris buenoi Genome Assembly 1.0

    The Baylor College of Medicine recently sequenced and annotated the Gerris buenoi genome as part of the i5k pilot project. This dataset presents the Gerris buenoi 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. The corresponding genome assembly in [GCA_001010745.1](https://www.ncbi.nlm.nih.gov/assembly/GCA_001010745.1/)

    Gerris buenoi genome annotations v0.5.3

      The Gerris buenoi genome was recently sequenced and annotated as part of the i5k pilot project by the Baylor College of Medicine. This dataset presents the Gerris buenoi 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 Gerris buenoi genome assembly 1.0. NOTE: This gene set is an unstable pre-release (v0.5.3), and was provided to facilitate manual curation and analyses before the official gene set is released. Gene identifiers from this gene set will likely not be maintained.

      Gerris buenoi Official Gene set v1.0

        The Gerris buenoi genome was recently sequenced and annotated as part of the i5k pilot project by the Baylor College of Medicine. The Gerris buenoi 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 (performed by Dan Hughes at Baylor College of Medicine) with manual annotations by the research community (done via the Apollo manual annotation software).

        Leptinotarsa decemlineata genome annotations v0.5.3

          This dataset presents the Leptinotarsa decemlineata 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 Leptinotarsa decemlineata genome assembly 1.0.

          Cimex Lectularius Official Gene Set v1.2

            The Baylor College of Medicine recently sequenced and annotated the Cimex lectularius genome as part of the i5k pilot project. The C. lectularius research community has manually reviewed and curated the computational gene predictions and generated an official gene set, OGSv1.2. This dataset presents the Cimex lectularius Official Gene Set (OGS) v1.1. The OGS is an integration of automatic gene predictions from MAKER with manual annotations by the research community.

            Leptinotarsa decemlineata Official Gene set v1.2

              The Leptinotarsa decemlineata genome was recently sequenced and annotated as part of the i5k pilot project by the Baylor College of Medicine. The L. decemlineata research community has manually reviewed and curated the computational gene predictions and generated an official gene set, OGSv1.2. OGSv1.1 is an integration of automatic gene predictions from Maker (performed by Dan Hughes at Baylor College of Medicine) with manual annotations by the research community (done via the Apollo manual annotation software). The coordinates of OGSv1.1 were converted to the latest genome assembly, GCF_000500325.1, using coordinates_conversion and remap-gff3, to generate OGSv1.2.