Benjamin Callahan

In this commit, `allowOneOff=FALSE` was incorrectly described in the updated help text. https://github.com/benjjneb/dada2/commit/3750df1940b6b206f0ee96a6fcd0daa667c4bb90 Thanks to @eoblyen for catching this: https://github.com/qiime2/q2-dada2/pull/146#issuecomment-1074265969

Inspired by [a comment in the Q2 forum](https://forum.qiime2.org/t/discussion-methods-for-removing-contaminants-and-cross-talk/5626/6): > I recently used decontam on a heavily contaminant-influenced dataset (mostly very low-biomass water samples). The prevalence method worked very well for...

Integrating microbiome package stub within dada2 tutorial?

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Hi microbiome team, Over in dada2 land we are interested in linking our package with other excellent Bioconductor microbiome packages. The primary way we have done this so far is...

As described here: https://github.com/qiime2/q2-dada2/issues/165

`plotErrors` improvements: Drop zero-observation points and scale points by number of observations

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These currently generate a warning and show up half-visible on the bottom of the plot as per ggplot2 default.

They are somewhat redundant, and perhaps would best be combined. However, priors might need its own presentation...

Propagate file paths to the output of derepFastq and dada

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This is a usefull bit if info to record, but even better it drops the need to bring along the files/derep objects separately when calling mergePairs.

Update Big Data workflow in light of recent package improvements

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A lot of the Big Data workflow has been baked into the standard operation of the package in recent version updates. It should be updated to reflect the current state...

Right now only 454/Ion-torrent are mentioned. Should perhaps also say something about single-end processing.

Update deprecated tutorials to make their deprecation clear

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Or consider deleting them entirely? Apparently deprecated tutorials from older versions of the package are showing up higher on some Google searches than the current version of the tutorial.