removePrimers: Removes primers and orients reads in a consistent direction.įastqFilter ( fn, fout, truncQ = 2, truncLen = 0, maxLen = Inf, minLen = 20, trimLeft = 0, trimRight = 0, maxN = 0, minQ = 0, ma圎E = Inf, rm.phix = TRUE, rm.lowcomplex = 0, orient.fwd = NULL, n = 1e+06, OMP = TRUE, qualityType = 'Auto', compress = TRUE, verbose = FALSE.removeBimeraDenovo: Remove bimeras from collections of unique sequences.plotQualityProfile: Plot quality profile of a fastq file.plotErrors: Plot observed and estimated error rates.plotComplexity: Plot sequence complexity profile of a fastq file.PacBioErrfun: Estimate error rates from transition counts in PacBio CCS.nwhamming: Hamming distance after Needlman-Wunsch alignment.noqualErrfun: Estimate error rates for each type of transition while.names-set-derep-ANY-method: Deactivate renaming of derep-class objects.names-set-dada-ANY-method: Deactivate renaming of dada-class objects.mergeSequenceTables: Merge two or more sample-by-sequence observation matrices.mergePairs: Merge denoised forward and reverse reads.makeTaxonomyFasta_SilvaNR: This function creates the dada2 assignTaxonomy training fasta.makeTaxonomyFasta_Silva: DEPRECATED in favor of 'makeTaxonomyFasta_SilvaNR'.makeTaxonomyFasta_RDP: This function creates the dada2 assignTaxonomy training fasta.makeSpeciesFasta_Silva: This function creates the dada2 assignSpecies fasta file for.makeSpeciesFasta_RDP: This function creates the dada2 assignSpecies fasta file for.makeSequenceTable: Construct a sample-by-sequence observation matrix.loessErrfun: Use a loess fit to estimate error rates from transition.learnErrors: Learns the error rates from an input list, or vector, of file.isShiftDenovo: Identify sequences that are identical to a more abundant.

isPhiX: Determine if input sequence(s) match the phiX genome.

isBimeraDenovoTable: Identify bimeras in a sequence table.

isBimeraDenovo: Identify bimeras from collections of unique sequences.

isBimera: Determine if input sequence is a bimera of putative parent.

inflateErr: Inflates an error rate matrix by a specified factor, while.

getUniques: Get the uniques-vector from the input object.

getSequences: Get vector of sequences from input object.

getErrors: Extract already computed error rates.

filterAndTrim: Filter and trim fastq file(s).

fastqPairedFilter: Filters and trims paired forward and reverse fastq files.

fastqFilter: Filter and trim a fastq file.

errBalancedR: An empirical error matrix.

errBalancedF: An empirical error matrix.derepFastq: Read in and dereplicate a fastq file.derepFasta: derepFasta creates a derep-class object from a fasta file, by.derep-class: A class representing dereplicated sequences.dada-class: The object class returned by 'dada'.dada: High resolution sample inference from amplicon data.collapseNoMismatch: Combine together sequences that are identical up to shifts.c-derep-method: Change concatenation of derep-class objects to list.c-dada-method: Change concatenation of dada-class objects to list.assignTaxonomy: Classifies sequences against reference training dataset.

assignSpecies: Taxonomic assignment to the species level by exact matching.

addSpecies: Add species-level annotation to a taxonomic table.

Dada2 rarify