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i5k Workspace@NAL
U.S. Department of Agriculture

i5k Workspace Project and Data Submission Overview

What is the i5k Workspace?

The i5k workspace is an inclusive genome portal for any "orphaned" arthropod genome project that would like to make use of our resources. We provide:

  • download services; 
  • BLAST; 
  • the JBrowse genome browser;
  • the Apollo manual curation software;
  • Manual annotation QA/QC and NCBI submission;
  • Mapped RNA-Seq;
  • Functional annotations.

If you want to learn more about the i5k Workspace, you can read our paper or view our presentations and posters. Please also refer to our data management and long-term management policy documents for information about the data types that we store and our long-term data management policy.

What is an i5k Workspace Project?

An i5k Workspace Project centers around an arthropod species and its genome assembly. This genome assembly must also be available from NCBI's RefSeq resource, with few exceptions. An i5k Workspace Project also contains gene predictions from that assembly - usually from NCBI's eukaryotic annotation pipeline - and data that were mapped to the assembly.
Genome communities use the i5k Workspace to visualize, share, and curate their genome project data. Often, an i5k Workspace project has an active curation community, which strives to improve their genome project using community expertise and the Apollo manual curation tool.
In some cases, an i5k Workspace Project will have multiple assemblies. In order to minimize confusion and duplication of effort, curation activity occurs only on one assembly at a time.

How do I start an i5k Workspace Project?

If you'd like to create an i5k Workspace project, please contact i5k@ars.usda.gov.

How do I add data to an existing i5k Workspace Project?

If you'd like to add data to an existing project, please contact i5k@ars.usda.gov.