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Type: New Feature
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Status: Closed
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Priority: Major
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Resolution: Fixed
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Affects Version/s: None
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Fix Version/s: 1.15
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Component/s: None
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Labels:None
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Tests Type:Functional/Unit
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Epic Link:
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Affect Type:Userdefined
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
- relates to
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UGENE-371 Integrate into UGENE another de novo assembly tool for short reads
- Closed
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UGENE-2040 Embed Mira assembler
- Closed