Citation

dada2-rs is a reimplementation of DADA2. If you use it, please cite the original work that describes the algorithm. Machine-readable citation metadata for this project lives in CITATION.cff at the repository root.

Cite the original DADA2 algorithm

• Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJA, Holmes SP. DADA2: High-resolution sample inference from Illumina amplicon data. Nature Methods. 2016;13:581–583. doi:10.1038/nmeth.3869
• Rosen MJ, Callahan BJ, Fisher DS, Holmes SP. Denoising PCR-amplified metagenome data. BMC Bioinformatics. 2012;13:283. doi:10.1186/1471-2105-13-283

Provenance & guidelines

This project follows the rewrites.bio guidelines as closely as possible, with the aim of ensuring the original DADA2 developers and contributors retain clear credit for their work, following the original implementation's details, including tests and benchmarks, and releasing as open source under the original licensing.

Results may differ slightly from R DADA2

Some implementation details (the R/C++ → Rust conversion, including the error models) cause small differences from R DADA2. We strive to reproduce results as closely as possible, and provide the ability to use R and/or Python for custom error-model analysis to more closely emulate the original implementation.