Welcome to Sidle

SMURF Implementation Done to acceLerate Effeciency

Sidle is a python version of the Short MUltiple Reads Framework (SMURF) algorithm originally developed by Fuks et al (2018) with a novel tree-building solution. This allows the reconstruction of multiple short, fragmented amplicons against a known database to improve the resolutionf of the reconstructed community over single amplicons.


If you use Sidle, 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
  1. 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

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