addSpecies              Add species-level annotation to a taxonomic
                        table.
assignSpecies           Taxonomic assignment to the species level by
                        exact matching.
assignTaxonomy          Classifies sequences against reference training
                        dataset.
collapseNoMismatch      Combine together sequences that are identical
                        up to shifts and/or length.
dada                    High resolution sample inference from amplicon
                        data.
dada-class              The object class returned by 'dada'
dada2-package           DADA2 package
derep-class             A class representing dereplicated sequences
derepFastq              Read in and dereplicate a fastq file.
errBalancedF            An empirical error matrix.
errBalancedR            An empirical error matrix.
errExtremeF             An empirical error matrix.
errExtremeR             An empirical error matrix.
errHmpF                 An empirical error matrix.
errHmpR                 An empirical error matrix.
evaluate_kmers          Generate the kmer-distance and the alignment
                        distance from the given set of sequences.
fastqFilter             Filter and trim a fastq file.
fastqPairedFilter       Filters and trims paired forward and reverse
                        fastq files.
getDadaOpt              Get DADA options
getSequences            Get vector of sequences from input object.
getUniques              Get the uniques-vector from the input object.
inflateErr              Inflates an error rate matrix by a specified
                        factor, while accounting for saturation.
isBimera                Determine if input sequence is a bimera of
                        putative parent sequences.
isBimeraDenovo          Identify bimeras from collections of unique
                        sequences.
isBimeraDenovoTable     Identify bimeras in a sequence table.
isPhiX                  Determine if input sequence(s) match the phiX
                        genome.
isShiftDenovo           Identify sequences that are identical to a more
                        abundant sequence up to an overall shift.
loessErrfun             Use a loess fit to estimate error rates from
                        transition counts.
makeSequenceTable       Construct a sample-by-sequence observation
                        matrix.
mergePairs              Merge denoised forward and reverse reads.
mergePairsByID          Merge forward and reverse reads after DADA
                        denoising, even if reads were not originally
                        ordered together.
mergeSequenceTables     Merge two or more sample-by-sequence
                        observation matrices.
nwalign                 Needlman-Wunsch alignment.
nwhamming               Hamming distance after Needlman-Wunsch
                        alignment.
plotComplementarySubstitutions
                        Plot Substitution Pairs from DADA Result
plotErrors              Plot observed error rates after denoising.
plotQualityProfile      Plot quality profile of a fastq file.
removeBimeraDenovo      Remove bimeras from collections of unique
                        sequences.
setDadaOpt              Set DADA options
show,derep-method       method extensions to show for dada2 objects.
tperr1                  An empirical error matrix.
uniques-vector          The named integer vector format used to
                        represent collections of unique DNA sequences.
uniquesToFasta          Write a uniques vector to a FASTA file
