# Accurate, high-resolution sample inference from amplicon sequencing data

## Documentation for package ‘dada2’ version 1.6.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

dada2-package | DADA2 package
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.
c-method | Change concatenation to list construction.
c-method | Change concatenation to list construction.
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'
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.
filterAndTrim | Filter and trim fastq file(s).
getDadaOpt | Get DADA options
getErrors | Extract already computed error rates.
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.
learnErrors | Learns the error rates from an input list, or vector, of file names or a list of 'derep-class' objects.
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.
names<--method | Deactivate renaming of dada-class objects.
names<--method | Deactivate renaming of derep-class objects.
noqualErrfun | Estimate error rates for each type of transition while ignoring quality scores.
nwalign | Needleman-Wunsch alignment.
nwhamming | Hamming distance after Needlman-Wunsch alignment.
plotComplementarySubstitutions | Plot Substitution Pairs from DADA Result
plotErrors | Plot observed and estimated error rates.
plotQualityProfile | Plot quality profile of a fastq file.
removeBimeraDenovo | Remove bimeras from collections of unique sequences.
setDadaOpt | Set DADA options
show-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
writeFasta-method | Writes a named character vector of DNA sequences to a fasta file. Values are the sequences, and names are used for the id lines.