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nhoffman / dada2-nf

A Nextflow pipeline for processing 16S rRNA sequences using dada2
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switching from cmalign to cmsearch #14

Closed crosenth closed 3 years ago

crosenth commented 4 years ago

Per Issue https://github.com/nhoffman/dada2-nf/issues/13

tholland commented 4 years ago

The only thing I would note is prior pipelines also used the -E 0.01 flag with cmsearch.

crosenth commented 4 years ago

@tholland - What was the -E flag used for in prior pipelines?

tholland commented 4 years ago

In our case I recall it produced better results to include the stricter threshold for matches, but I'd have to find the validation for it again to see how much of a difference it makes.