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Try minimap2 splice #66

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priyanka-surana opened this issue Mar 17, 2023 · 1 comment
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Try minimap2 splice #66

priyanka-surana opened this issue Mar 17, 2023 · 1 comment
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@reichan1998
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enhancement Improvement of the existing features help wanted Open to anyone interested question Further information is requested user request Requests made by users and public

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@priyanka-surana
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Description of feature

The BlastN step in PacBio read filtering is slow. A suggestion from Yumi was that we could try minimap2 splice.

Compare run time between BlastN vs Minimap2 Splice and select the more efficient option.
@priyanka-surana priyanka-surana added the enhancement Improvement of the existing features label Mar 17, 2023
@priyanka-surana priyanka-surana added the user request Requests made by users and public label Jun 27, 2023
@muffato muffato added feature Requests for new features and removed enhancement Improvement of the existing features labels Jun 1, 2024
@muffato muffato added help wanted Open to anyone interested question Further information is requested enhancement Improvement of the existing features and removed feature Requests for new features labels Jun 17, 2024
@reichan1998 reichan1998 self-assigned this Jul 30, 2024
@reichan1998 reichan1998 mentioned this issue Aug 6, 2024
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@reichan1998 reichan1998 linked a pull request Aug 6, 2024 that will close this issue
Replace BlastN by Minimap2 splice. #104
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@tkchafin
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Closing as we have determined minimap splice to not work as an alternative

@tkchafin tkchafin mentioned this issue Sep 10, 2024
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@reichan1998 reichan1998

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enhancement Improvement of the existing features help wanted Open to anyone interested question Further information is requested user request Requests made by users and public
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Genome After Party
Status: Done
readmapping
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Replace BlastN by Minimap2 splice. reichan1998/readmapping
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@muffato @tkchafin @priyanka-surana @reichan1998