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sanjaynagi / AmpSeeker

A snakemake workflow for amplicon sequencing
https://sanjaynagi.github.io/AmpSeeker/
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speed up snp-dataframe nb #113

Closed sanjaynagi closed 9 months ago

sanjaynagi commented 9 months ago

Something in here is super slow (for amplicon snps). its the slowest part of the whole workflow which is not acceptable.

code looks overly complex, lets fix.

sanjaynagi commented 9 months ago

Last resort can even be to remove the snps across amplicons. but probably not necessary.

sanjaynagi commented 9 months ago

Resolved by only making snp dataframe for targets by default