A QIIME 2 implementation of SMURF.
Full documentation on read the docs
q2-sidle requires a QIIME 2 enviroment. Install QIIME2 according to the method that works best for your system.
Sidle depends on two conda libraries, dask
and regex
, as well as the RESCRIPt qiime2 plugin. To install the plugin, start with adding the addtional conda libraries:
conda install dask regex
conda install -c conda-forge -c bioconda -c qiime2 -c defaults xmltodict
Next, you will need the RESCRIPt and sidle plugins.
pip install git+https://github.com/bokulich-lab/RESCRIPt.git
pip install git+https://github.com/jwdebelius/q2-sidle
Finally, update your qiime libraries.
qiime dev refresh-cache
Please see our tutorial on read the docs
Problem? Suggestion? Technical errors and user support requests can be filed on the QIIME 2 Forum.
If you use Sidle in your reserach, please cite:
-
Debelius, J.W.; Robeson, M.; Lhugerth, L.W.; Boulund, F.; Ye, W.; Engstrand, L. "A comparison of approaches to scaffolding multiple regions along the 16S rRNA gene for improved resolution." Preprint in BioRxiv. doi: 10.1101/2021.03.23.436606
-
Fuks, G.; Elgart, M.; Amir, A.; Zeisel, A.; Turnbaugh, P.J., Soen, Y.; and Shental, N. (2018). "Combining 16S rRNA gene variable regions enables high-resolution microbial community profiling." Microbiome. 6: 17. doi: 10.1186/s40168-017-0396-x