unoisenim — Nim library for amplicon sequencing analysis.
Provides efficient implementations of USEARCH algorithms for processing 16S/ITS amplicon sequencing data:
- unoisenim/unoise_algo — UNOISE3 error correction and ZOTU clustering
- unoisenim/uchime2_algo — UCHIME2 chimera detection
- unoisenim/sintax_algo — SINTAX taxonomic classification
- unoisenim/nbc_algo — Naive Bayesian Classifier (RDP-style) taxonomy
- unoisenim/utils — Utility helpers for FASTA label parsing
References
- Edgar RC. UNOISE2: improved error-correction for Illumina 16S and ITS amplicon sequencing. bioRxiv 081257; doi: 10.1101/081257
- Edgar RC. SINTAX: a simple non-Bayesian taxonomy classifier for 16S and ITS sequences. bioRxiv 074161; doi: 10.1101/074161
- Wang Q, Garrity GM, Tiedje JM, Cole JR. Naive Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy. Appl Environ Microbiol. 2007; doi: 10.1128/AEM.00062-07
Exports
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parseSize, Centroid, extractKmers, UnoiseSeq, editDistanceLimit, unoise, globalAlign, AlignPath, getLeftRight, uchime, SintaxHit, SintaxIndex, postingLen, postingFirst, initSintaxState, buildIndex, sintaxWithState, extractTaxRanks, rc, classifyOneDir, SintaxState, sintax, NbcKmerSize, reverseComplement, NbcIndex, buildNbcIndex, NbcHit, parseTaxRanks, nbc, phixSeqLen, phixScore, phixKmers, isPhix