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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

22 datasets

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/).

    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.

      Data from: Integrating classical genetics with chromosome-scale genome assembly to characterize a genetic sexing system in Bactrocera cucurbitae (Diptera: Tephritidae)

        This data supports the manuscript "Integrating classical genetics with chromosome-scale genome assembly to characterize a genetic sexing system in Bactrocera cucurbitae (Diptera: Tephritidae)". The melon fly, Bactrocera cucurbitae, is a destructive agricultural pest and is the subject of strict quarantines that are enforced to prevent its establishment outside of its current geographic range. In addition to quarantine efforts, additional control measures are necessary for its eradication in the case of invasion to agriculturally rich areas. The sterile insect technique (SIT) has been effective in the control of several invertebrate pest species, and is part of a management strategy that regulatory agencies would like to expand to other important pests such as the melon fly.

        Pachypsylla venusta genome assembly v1.0

          The Baylor College of Medicine has sequenced and annotated the Pachypsylla venusta genome as part of the i5k pilot project. This dataset presents the Pachypsylla venusta 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.