# Qiime2 ConQuR Plugin for Batch Correction (or alternative)

**URL:** https://forum.qiime2.org/t/qiime2-conqur-plugin-for-batch-correction-or-alternative/33218
**Category:** General Discussion
**Tags:** batch-effects
**Created:** [May 31, 2025, 6:39am UTC](https://forum.qiime2.org/t/qiime2-conqur-plugin-for-batch-correction-or-alternative/33218 "2025-05-31T06:39:42Z")
**Posts on this page:** 3
**Page:** 1

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### Author: ![charlesalexandreroy](https://forum.qiime2.org/user_avatar/forum.qiime2.org/charlesalexandreroy/32/20974_2.png) [@charlesalexandreroy](https://forum.qiime2.org/u/charlesalexandreroy)
#### Post date: [May 31, 2025, 6:39am UTC](https://forum.qiime2.org/t/qiime2-conqur-plugin-for-batch-correction-or-alternative/33218/1 "2025-05-31T06:39:42Z")

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Hi all!

I recently came across the ConQuR tool ([paper](https://www.nature.com/articles/s41467-022-33071-9), [GitHub](https://github.com/wdl2459/ConQuR?tab=readme-ov-file)) for dealing with microbiome batch effects, and it looks pretty useful.

I was wondering whether a Qiime2 plugin exists for it, and if not, whether one might be in development?

If not, as described in their [vignette](https://wdl2459.github.io/ConQuR/ConQuR.Vignette.html) (or [manual](https://github.com/wdl2459/ConQuR/blob/main/ConQuR_2.0.pdf)), 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 (if anywhere) if I were to unzip a .qza file to process it with ConQuR?

I am also interested if anyone knows about any other tools that might be as good as (or better than) ConQuR.

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### Author: ![Nicholas\_Bokulich](https://forum.qiime2.org/user_avatar/forum.qiime2.org/nicholas_bokulich/32/19937_2.png) [@Nicholas\_Bokulich](https://forum.qiime2.org/u/Nicholas_Bokulich)
#### Post date: [May 31, 2025, 6:53am UTC](https://forum.qiime2.org/t/qiime2-conqur-plugin-for-batch-correction-or-alternative/33218/2 "2025-05-31T06:53:24Z")

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Hi @charlesalexandreroy ,  
Welcome to the forum!

A few years back there was a QIIME 2 plugin, [q2-perc-norm](https://github.com/cduvallet/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](https://forum.qiime2.org/t/case-control-studies-and-batch-correction-community-tutorial/7325):
>
> Dear QIIME2 Community, [Christian Diener](https://gibbons.systemsbiology.org/bio/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.](https://github.com/Gibbons-Lab/ccmb_workshop) 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](https://amplicon-docs.qiime2.org/en/latest/) 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!

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### Author: ![charlesalexandreroy](https://forum.qiime2.org/user_avatar/forum.qiime2.org/charlesalexandreroy/32/20974_2.png) [@charlesalexandreroy](https://forum.qiime2.org/u/charlesalexandreroy)
#### Post date: [June 4, 2025, 4:04am UTC](https://forum.qiime2.org/t/qiime2-conqur-plugin-for-batch-correction-or-alternative/33218/3 "2025-06-04T04:04:35Z")

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Edit:  
Actually, scratch the below. It seems that the author had a deadline and wasn't able to respond initially, but they are back now. They said they would look into making a Qiime2 plugin and are otherwise helping me get ConQuR to work for my dataset.

* * *

Thanks @Nicholas_Bokulich!

In case anyone else ends up here, after trying to get ConQuR to work for a few days, I think I am ready to give up on it. Unfortunately, even though it was published in Nature less than 3 years ago, it appears to be abandoned. At least, I'm not hearing back from the author via GitHub or email, and I'm experiencing an endless series of bugs as I try to get it working.

I'll see if q2-perc-norm can do the job for me.