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  1. IGB
  2. IGBF-2538

Support CSI tabix index for very large genomes

        Details

        • Type: New Feature
        • Status: To-Do (View Workflow)
        • Priority: Major
        • Resolution: Unresolved
        • Affects Version/s: None
        • Fix Version/s: None
        • Labels:
          None

          Description

          Larger genomes, e.g., bread wheat, cannot be indexed using .bai (BAM) or .tbi (tabix) files due to size.

          There is an alternative type of index called "csi" that can be used instead. It does not have the same size limitation.

          See: https://www.biostars.org/p/111984/

          For this new feature, enable IGB to support partial data loading of files indexed using tabix -C (which creates a .csi index instead of a .tbi index).

          See attached for example BED file with csi index.

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              Issue Links

              relates to

              Task - A task that needs to be done. IGBF-2333 Add wheat genome to IGB quickload system

              • Major - Major loss of function.
              • Closed

              Task - A task that needs to be done. IGBF-2548 Investigate: Why do wheat gene models fail to load

              • Major - Major loss of function.
              • Closed

              Task - A task that needs to be done. IGBF-2333 Add wheat genome to IGB quickload system

              • Major - Major loss of function.
              • Closed

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                  • Assignee:
                    Unassigned
                    Reporter:
                    ann.loraine Ann Loraine
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                    Dates

                    • Created:
                      Updated: