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AmpliconSuite / AmpliconSuite-pipeline

A quickstart tool for AmpliconArchitect. Performs all preliminary steps (alignment, CNV calling, seed interval detection) required prior to running AmpliconArchitect. Previously called PrepareAA.
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Missing seed_trimmer.py in the scripts directory #36

Closed solo7773 closed 1 year ago

solo7773 commented 1 year ago

Hi Jens,

Yesterday I updated from 0.13x to 0.1477, but there is no seed_trimmer.py any longer in the scripts directory. According to GUIDE.md, this script can filter CNV segments > 10 Mbp.

Unfortunately, I have deleted all the 0.13x files. Since I implement the AA pipeline manually myself, could you add the script back to the repository, or provide a workaround?

Many thanks, Nan

jluebeck commented 1 year ago

Hi Nan,

The older versions of PrepareAA can be accessed by visiting the version history of the repo on GitHub, or from the previous docker images.

Please keep in mind though that the reason we no long provide the standalone script is that there is a module now embedded with PrepareAA.py to handle these cases by default, and also improve filtering of arm-level chromosomal abnormalities which are likely not real focal amps. We believe the current solution in 0.1477 is better than what was presented in 0.13xx.

Thanks, Jens

solo7773 commented 1 year ago

Hi Jens,

Thank you very much. I see. I will use the 0.1477 now.

Best wishes, Nan