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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

81 datasets

Diaphorina citri MCOT transcriptome

    The Diaphorina citri MCOT v1.0 transcriptome is a genome independent transcriptome assembly that provides a comprehensive set of gene models and was performed with the MCOT pipeline where transcripts from Maker, Cufflinks, Trinity and Oases pipelines are combined.

    Diaphorina citri Official Gene Set v1.0

      This gene set (OGS v1.0) combines both automatically predicted and manually curated gene models. This community effort produced 530 manually curated gene models across developmental, physiological, RNAi regulatory, and immunity-related pathways. As previously shown in the pea aphid, RNAi machinery genes putatively involved in the microRNA pathway have been specifically duplicated. A comprehensive transcriptome enabled us to identify a number of gene families that are either missing or misassembled in the draft genome.

      Leptinotarsa decemlineata genome assembly 1.0

        This dataset presents the Leptinotarsa decemlineata 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](http://www.ncbi.nlm.nih.gov/assembly/GCA_000696205.1)

        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.

          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.

            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).

              Hyalella azteca Genome Assembly 1.0

                The Baylor College of Medicine recently sequenced and annotated the Hyalella azteca genome as part of the i5k pilot project. The Hyalella azteca research community has manually reviewed and curated the computational gene predictions and generated an official gene set, OGSv1.0. This dataset presents the Hyalella azteca 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 NCBI is [GCA_000764305.1](https://www.ncbi.nlm.nih.gov/assembly/GCA_000764305.1).

                Hyalella azteca Genome Annotations v0.5.3

                  The Baylor College of Medicine recently sequenced and annotated the Hyalella azteca genome as part of the i5k pilot project. This dataset presents the Hyalella azteca 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 Hyalella azteca genome assembly 1.0. Further annotation method details will be available in a forthcoming publication.

                  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.