Nim

unoisenim

A Nim library implementing USEARCH-compatible algorithms for 16S/ITS amplicon sequencing — denoising, chimera detection, and taxonomic classification.

Nim ≥ 2.0 bioinformatics amplicon GPL 3.0

Install

$ nimble install unoisenim

Modules

unoisenim
Top-level module — imports and re-exports all sub-modules for convenience.
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unoisenim/unoise_algo
UNOISE3 error correction and Zero-radius OTU (ZOTU) clustering. Sequences are denoised using the UNOISE skew formula and banded Levenshtein distance.
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unoisenim/uchime2_algo
UCHIME2 chimera detection via global pairwise alignment and left/right scoring against centroid sequences.
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unoisenim/sintax_algo
SINTAX taxonomic classification using k-mer bootstrapping — a fast, non-Bayesian alternative to RDP for 16S and ITS sequences.
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unoisenim/nbc_algo
Naive Bayesian Classifier (RDP-style) for rapid taxonomic assignment of rRNA amplicon sequences.
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unoisenim/utils
Utility helpers for FASTA label parsing (e.g. abundance annotations).
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UNOISE/UCHIME algorithm
Summary card of the UNOISE/UCHIME algorithm.
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SINTAX algorithm
Summary card of the SINTAX algorithm.
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Links

References