Qiime2 ConQuR Plugin for Batch Correction (or alternative)

[Nicholas_Bokulich]

Hi @charlesalexandreroy ,
Welcome to the forum!

A few years back there was a QIIME 2 plugin, q2-perc-norm, designed for batch correction. You can see a post about it here with some more useful links:

Case-Control Studies and Batch Correction: Community Tutorial

Dear QIIME2 Community, Christian Diener and myself taught a QIIME2 workshop at the University of British Columbia at Kelowna on December 3rd, 2018. Christian has included all of our workshop materials, including a step-by-step walk-through, input files, and output files on github: GitHub - Gibbons-Lab/ccmb_workshop: Data and materials for the CCMB workshop on Cloud Computing and Microbiome Bioinformatics. We hope you find our tutorial useful. It walks through analysis of several 16S colorectal…

I am not aware of a plugin for ConQuR, but it certainly sounds useful. I would recommend contacting the authors of ConQuR to discuss the idea — if you or they are interested in developing such a plugin, you can let us know on the forum if you need help getting started with plugin development.

@charlesalexandreroy

the tool starts from a n (samples, rows) by p (taxa, cols) counts matrix. Where in the Qiime2 pipeline would an output like that be generated

This would be a feature table, and more specifically a FeatureData[Frequency] artifact. Many different QIIME 2 plugins produce and work with these but the most basic steps to generate a feature table (and specifically one where the features are taxonomic groups) would be:

1. denoise and/or cluster your sequences, e.g., with q2-dada2, q2-deblur, or q2-vsearch (all of these will generate feature tables from demultiplexed sequence data; see the amplicon-docs for more usage details)
2. perform taxonomy classification of your representative sequences with q2-feature-classifier
3. use the q2-taxa plugin to collapse your feature table by taxonomy. The output will be a feature table (count matrix) of samples X taxa.

Good luck!