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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

28 datasets

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/.

    Orussus abietinus Official Gene Set OGSv1.0

      The Orussus abietinus genome was recently sequenced and annotated as part of the i5k pilot project by the Baylor College of Medicine. The Orussus abietinus research community has manually reviewed and curated the computational gene predictions and generated an official gene set, OGSv1.0. The general procedure for generating this OGS is outlined here: https://github.com/NAL-i5K/I5KNAL_OGS/wiki. OGSv1.0 was generated by merging gene set OABI-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.

      Athalia rosae Official Gene Set OGSv1.0

        The Athalia rosae genome was recently sequenced and annotated as part of the i5k pilot project by the Baylor College of Medicine. The Athalia rosae research community has manually reviewed and curated the computational gene predictions and generated an official gene set, OGSv1.0. The general procedure for generating this OGS is outlined here: https://github.com/NAL-i5K/I5KNAL_OGS/wiki. OGSv1.0 was generated by merging gene set AROS-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.

        Orussus abietinus genome annotations v0.5.3

          This dataset presents the Orussus abietinus gene set BCM_v_0.5.3. RNA-Seq data was used with additional protein homology data for a MAKER automated annotation of the Orussus abietinus genome assembly 1.0.

          Athalia rosae genome annotations v0.5.3

            This dataset presents the Athalia rosae gene set BCM_v_0.5.3. RNA-Seq data was used with additional protein homology data for a MAKER automated annotation of the Athalia rosae genome assembly 1.0.

            Ephemera danica Official Gene Set ephdan_OGSv1.0

              This dataset presents the *Ephemera danica* Official Gene Set (OGS) v1.0. The OGS is an integration of automatic gene predictions from *Ephemera danica* genome annotations v0.5.3, with manual annotations by the research community. Manual and automated annotations were lifted over from genome assembly *Ephemera danica* genome assembly v1.0 to genome assembly Edan_2.0 using the coordinates_conversion and remap-gff3 programs.

              Ephemera danica manual annotations on genome assembly Edan_1.0

                This dataset presents manual annotations of Ephemera danica genome annotations v0.5.3 and genome assembly v1.0. Manual annotations were performed by individual annotators in the Apollo software at the i5k Workspace@NAL, and QC'd via the GFF3toolkit software and manual inspection. Manual annotations are presented here on the original coordinate system of genome assembly v1.0.

                Halyomorpha halys genome annotations v0.5.3

                  This dataset presents the Halyomorpha halys gene set BCM_v_0.5.3. RNA-Seq data was used with additional protein homology data for a MAKER automated annotation of the Halyomorpha halys genome assembly 1.0. If you wish to use this dataset, please follow the Baylor College of Medicine's conditions for data use: https://www.hgsc.bcm.edu/bcm-hgsc-conditions-use

                  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/).

                    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.