I am happy to announce that the SRS QIIME 2 plugin is out!
Here follows a short guide on how to install and use q2-srs (or go to the full tutorial).
qiime2>=2020.8 environment by running (or equivalent):
conda activate qiime2-2020.8
- Option 1 - To install from conda, run:
conda install -c vitorheidrich q2_srs
- Option 2 - To install from the repository, run:
pip install git+https://github.com/vitorheidrich/q2-srs.git
Check for successful installation by running
q2-srs features two
qiime srs SRS- performs SRS normalization at a user-defined number of reads per sample
qiime srs SRScurve- draws alpha diversity rarefaction curves for SRS-normalized data (instead of rarefied data)
We strongly encourage you to explore the SRS Shiny app, that is specifically designed for q2-srs users.
In order to normalize your samples to the same number of reads using SRS, we recommend running
SRScurve first so you can determine a good normalization cut-off for your data. This normalization cut-off is called Cmin (see the SRS paper for details).
Alternatively (and complementarily) to
SRScurve, we strongly advise for the use of the SRS Shiny app for the determination of Cmin.
Once you have chosen an adequate Cmin, run
SRS with the Cmin that suits your data.
The output of
SRS will be an OTU/ASV table SRS-normalized at Cmin reads per sample that is ready for the next steps of your pipeline.
Please go to the full tutorial to see the plugin in action.
Reporting an issue
Since q2-srs is just coming out please be watchful for bugs and, if possible, report them to us here in the forum or by opening an issue.