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  1. UGENE
  2. UGENE-371

Integrate into UGENE another de novo assembly tool for short reads

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    Details

    • Type: New Feature
    • Status: Closed
    • Priority: Major
    • Resolution: Won't Fix
    • Affects Version/s: None
    • Fix Version/s: None
    • Component/s: NGS
    • Affect Type:
      Userdefined

      Description

      Currently, SPAdes tool is integrated into UGENE. However it has some limitations:
      1) SPAdes was initially designed for small genomes.
      2) It is not available on WIndows.

      So, please add support for another de novo assembly tool which is targeted on aligning short-reads ~ 30-100 bp (e.g. Illumina reads)
      Consider candidates:
      1) Velvet
      2) SSAKE
      3) Euler
      4) MIRA
      ...
      Good review is available here:
      http://www.ncbi.nlm.nih.gov/pubmed/21559467

        Attachments

          Issue Links

          relates to

          Improvement - An improvement or enhancement to an existing feature or task. UGENE-4222 Investigate NGS data de novo assembling

          • Major - Major loss of function.
          • Closed

          New Feature - A new feature of the product, which has yet to be developed. UGENE-2833 de novo assembler integration

          • Major - Major loss of function.
          • Closed

          New Feature - A new feature of the product, which has yet to be developed. UGENE-2040 Embed Mira assembler

          • Trivial - Cosmetic problem like misspelt words or misaligned text.
          • Closed

            Activity

              People

              Assignee:
              Unassigned
              Reporter:
              kokonech Konstantin Okonechnikov (Inactive)
              Watchers:
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                Dates

                Created:
                Updated:
                Resolved: