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  1. UGENE
  2. UGENE-2833

de novo assembler integration

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    Details

    • Type: New Feature
    • Status: Closed
    • Priority: Major
    • Resolution: Fixed
    • Affects Version/s: None
    • Fix Version/s: 1.15
    • Component/s: None
    • Labels:
      None
    • Tests Type:
      Functional/Unit
    • Epic Link:
    • Affect Type:
      Userdefined

      Description

      Description: Assembling genomes de novo is an essential step not only for genomes for which the reference sequence is unknown, but also for double-checking contigs generated by a short read aligner. There are dozens of de novo assemblers: Velvet, SOAP-denovo, Mira, etc.
      Links: http://seqanswers.com/wiki/De-novo_assembly (list of assemblers)
      Scope:
      Integrate a de novo assembler into UGENE and provide a GUI for it. The integrations steps are the following:
      1. Select a de novo assembler. Make sure that an assembler can be run on a PC.
      2. Integrate the assembler and develop a GUI similar to the GUI that exists in UGENE for short reads alignment with read selection, parameter settings and showing the result in Assembly Browser.
      3*. Add the corresponding workflow element in Workflow Designer

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              Assignee:
              vaskin Yura Vaskin
              Reporter:
              vaskin Yura Vaskin
              Assigned Tester:
              Artyom Savchenko
              Watchers:
              2 Start watching this issue

                Dates

                Created:
                Updated:
                Resolved: