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jwdebelius / q2-sidle

A QIIME 2 implementation of SMURF
BSD 3-Clause "New" or "Revised" License
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q2-sidle

A QIIME 2 implementation of SMURF.

Full documentation on read the docs

Installation

q2-sidle requires a QIIME 2 enviroment. Install QIIME2 according to the method that works best for your system.

Sidle depends on the dask library, as well as the RESCRIPt qiime2 plugin. To install the plugin, start with adding the addtional conda libraries:

conda install dask
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

Tutorial

Please see our tutorial on read the docs

Getting Help

Problem? Suggestion? Technical errors and user support requests can be filed on the QIIME 2 Forum.

Citation

If you use Sidle in your reserach, please cite:

  1. 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

  2. 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