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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

112 datasets

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.

    Frankliniella occidentalis Official Gene Set OGSv1.1

      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.

      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.

        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).

          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.

            Halyomorpha halys Official Gene Set v1.2

              This dataset presents the Halyomorpha halys Official Gene Set (OGS) v1.2. OGSv1.2 and is an update of Halyomorpha halys OGSv1.1 (https://doi.org/10.15482/USDA.ADC/1504240) to the coordinates of genome assembly GCA_000696795.3 (https://www.ncbi.nlm.nih.gov/assembly/GCA_000696795.3) using https://github.com/NAL-i5K/coordinates_conversion/.

              Halyomorpha halys Official Gene Sets v1.0 and v1.1

                This dataset presents the *Halyomorpha halys* Official Gene Set (OGS) v1.0 and v1.1. The OGS is an integration of automatic gene predictions from NCBI's eukaryotic annotation pipeline, [NCBI Halyomorpha halys Annotation Release 100](https://www.ncbi.nlm.nih.gov/genome/annotation_euk/Halyomorpha_halys/100/), with manual annotations by the research community (performed via the Apollo manual curation software, http://genomearchitect.org/).