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Refactor trimming and filtering #49

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cjfields opened this issue Oct 28, 2024 · 0 comments
Open

Refactor trimming and filtering #49

cjfields opened this issue Oct 28, 2024 · 0 comments
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DSL2 Prioritize for DSL2 implementation

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@cjfields
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We are performing a few different variations of trimming and filtering, with many of these using mashups of cutadapt and DADA2's filterAndTrim.

  • Illumina paired-end (non-variable, overlapping or non-overlapping) - only DADA2 filterAndTrim (16S V4, V3-V5)
  • Illumina paired-end variable, overlapping + non-overlapping - cutadapt + DADA2 filterAndTrim (ITS)
  • PacBio HiFi - cutadapt + filterAndTrim (full-length 16S)

It's worth setting these up as subworkflows based on the above choices; this would of course require DSL2.
@cjfields cjfields added the DSL2 Prioritize for DSL2 implementation label Oct 28, 2024
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@cjfields