the pooled option to the --p-chimera-method parameter in q2-dada2

[maisey]

Thanks for the update! I was wondering if you could provide more details or point me to other discussions/ papers regarding why the dada2 --p-chimera-method pooled should not be used with the other parameter options currently available in qiime? Under what circumstances would it make sense to use --p-chimera-method pooled?

[colinbrislawn (Colin J Brislawn)]

From the DADA2 GitHub: Differences in chimera detection based on dataset structure · Issue #1942 · benjjneb/dada2 · GitHub

From the qiime2 plugin for dada2 on github: Add warning when pooling method and chimera detection method are misaligned · Issue #165 · qiime2/q2-dada2 · GitHub

@maisey

Under what circumstances would it make sense to use --p-chimera-method pooled?

The pooled chimera detection method should only be used if using pooled denoising. It should not be used with the default denoising (independent) or with pseudo-pooling.