# Mock community assessment and quality control? **URL:** https://forum.qiime2.org/t/mock-community-assessment-and-quality-control/18776 **Category:** General Discussion **Created:** [March 8, 2021, 2:57pm UTC](https://forum.qiime2.org/t/mock-community-assessment-and-quality-control/18776 "2021-03-08T14:57:26Z") **Posts on this page:** 1 **Showing post:** 2
### 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: [March 8, 2021, 3:22pm UTC](https://forum.qiime2.org/t/mock-community-assessment-and-quality-control/18776/2 "2021-03-08T15:22:38Z")
Welcome to the forum, @bloman2 ! This is a great General Discussion topic, and those are some great ideas. > [@bloman2](#): > > beyond looking at whether or not the output is close to “expected”, How are you performing this comparison? If you are not already, you could use some quantitative methods to perform this comparison, e.g., to measure how accurately your mock community represents the expected results. See the "visualizers" section of this plugin: > **[quality-control — QIIME 2 2021.2.0 documentation](https://docs.qiime2.org/2021.2/plugins/available/quality-control/)** We have a tutorial demonstrating how to use some of these actions here: > [@Fungal ITS analysis tutorial](https://forum.qiime2.org/t/fungal-its-analysis-tutorial/7351): > > Fungal ITS analysis, mock communities, and more fun NOTE: This tutorial was written in a QIIME 2 2018.11 environment. It is not guaranteed to work with earlier or later versions of QIIME 2. This tutorial was compiled as a working exercise for a [QIIME 2 workshop](https://workshops.qiime2.org/microbiome-bioinformatics-qiime-2-2018-12-12/) in December 2018, and does not represent the only possible fungal ITS workflow with QIIME 2, or even a benchmarked protocol recommendation. See other tutorials, e.g., the [q2-itsxpress tutorial](https://forum.qiime2.org/t/q2-itsxpress-a-tutorial-on-a-qiime-2-plugin-to-trim-its-sequences/5780) for other fungal ITS analysis options in QII… Mock communities never look perfect (because of the various sources of bias including those you list) but these methods can be used to get a sense of overall quality... in practice, though, the first time you use a mock community you cannot tell whether its accuracy reflects the quality of the mock community used, or the quality of the run. So you put the same community on every run you do, and you can detect when the quality degrades (indicating a run error) as shown in this paper: > **[Taxon Disappearance from Microbiome Analysis Reinforces the Value of Mock...](https://pmc.ncbi.nlm.nih.gov/articles/PMC5883066/)** > > Despite the routine use of standards and blanks in virtually all chemical or physical assays and most biological studies (a kind of “control”), microbiome analysis has traditionally lacked such standards. Here we show that unexpected problems of ... This sort of process (using mock communities as a "canary in the coal mine") would accomplish this idea: > [@bloman2](#): > > give some sort of confidence value on the data as a whole? As for this idea: > [@bloman2](#): > > Is there potential for a future QIIME2 tool that would help correct sample data based on mock community results There is definitely room for improvement. I plan to update q2-quality-control at some point very soon, including to add this method (which uses negative controls, not mock communities): > **[Introduction to decontam](https://benjjneb.github.io/decontam/vignettes/decontam_intro.html)** I think I saw a publication in the past 2 years that used mock communities in a similar way, but I cannot find it now. One issue with using mock communities for this is that they can have their own issues — misannotation, poor contruction, poor quantification, contamination, etc — that are separate from the sequencing run. These can of course be controlled and validated, and validated mock communities can be purchased commercially (maybe this is what you are using), but they still poorly reflect the diversity of real samples so there may be issues with using mock communities for "denoising" data (data correction), as you describe. So long story short is that I recommend combining negative and positive controls as run standards, and negative controls can certainly be used for decontaminating data, mock communities for assessing data "quality" (with the caveats considered above). P.S., here is some relevant discussion from the forum past: > [@QC/benchmark Qiime2 on Mock community](https://forum.qiime2.org/t/qc-benchmark-qiime2-on-mock-community/2843): > > Qiime2 is a great tool. Before we put it into our production, we would like do some QC and benchmark on mock community. So we purchased zymo mix, ([https://www.zymoresearch.com/zymobiomics-community-standard](https://www.zymoresearch.com/zymobiomics-community-standard)), prepared DNA (used two different library prep kits) and whole cells (used two different DNA extraction methods and one library kit). Based on the user guide of Zymo, although all should have 12% of each bacterial component, the theoretical composition should be expected at Pseudomonas aerug… > [@Help! Too many taxa in mock community - how to interpret or how to deal with it?](https://forum.qiime2.org/t/help-too-many-taxa-in-mock-community-how-to-interpret-or-how-to-deal-with-it/10792/2): > > Hi @timpiel, welcome to the QIIME 2 community! I will start with few basic observations about mock communities: we almost never see perfect replication of expected results! exogenous contamination (e.g., in reagents, library preps) and cross-contamination (e.g., from other samples in your sequencing run) are common issues leading to observation 1 Index hopping and other technical errors can also lead to spurious detection of false-positives in your samples Primer bias and other issues can ser… > [@Discussion: methods for removing contaminants and cross-talk](https://forum.qiime2.org/t/discussion-methods-for-removing-contaminants-and-cross-talk/5626): > > Just to add further to this discussion, I've previously used decontam prior to it being incorporated into QIIME 2, and whilst I'm a huge fan of the principles it's built around, it didn't work fantastically for my samples. I will caveat that as I did only attempt the prevalence method with 2 negative controls (one kit negative and one sequencing negative) for around 20 samples, which is likely too low a number of controls to have any real statistical power, I'm not sure what the ideal number of … --- _[View the full topic](https://forum.qiime2.org/t/mock-community-assessment-and-quality-control/18776)._