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  1. UGENE
  2. UGENE-5270

UGENE mapper for Sanger data

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    Details

    • Type: New Feature
    • Status: Closed
    • Priority: Critical
    • Resolution: Fixed
    • Affects Version/s: 1.23
    • Fix Version/s: 1.27
    • Component/s: Basic-MSA, Basic-Nucl
    • Labels:
    • Story Points:
      8
    • Epic Link:
    • Sprint:
      DEV-24-1, DEV-24-2
    • Affect Type:
      Userdefined

      Description

      Implement the algorithm to map Sanger reads on reference based on Blast.

      There is an algorithm to align Sanger reads in UGENE based on KAlign and Smith-Waterman aligners. In the first step it aligns a read to the reference with KAlign to locate its approximate location. Secondly, it aligns a read to the reference region, located in the first step, using Smith-Waterman algorithm to locate an exact location of the read. Thirdly, it merges all aligned reads into a single msa.

      A new algorithm should be the same, except the first step: approximate reads positions should be calculated with BLAST instead of KAlign. So, whole algorithm will contain next steps:
      1. Create a BLAST database using the reference.
      2. Do a query to the BLAST database with a read. Get an approximate location from the response. Do it for every read.
      3. Calculate an exact location using Smith-Waterman algorithm. Do it for every read.
      4. Merge all reads into a single msa.

      The first step of the already existing algorithm is replaced with two steps. BLAST is much more faster than KAlign, but it is still not enough precise.

      Implement the new algorithm based on the AlignToReferenceTask.

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              Assignee:
              epushkova Eugenia Pushkova [X] (Inactive)
              Reporter:
              epushkova Eugenia Pushkova [X] (Inactive)
              Assigned Tester:
              Kirill Rasputin
              Watchers:
              3 Start watching this issue

                Dates

                Created:
                Updated:
                Resolved: