dada2: Accurate, high-resolution sample inference from amplicon sequencing data
Version 1.4.0

The dada2 package infers exact sequence variants (SVs) from amplicon data, replacing the coarser and less accurate OTU clustering approach. The dada2 pipeline takes as input demultiplexed fastq files, and outputs the sequence variants and their sample-wise abundances after removing substitution and chimera errors. Taxonomic classification is available via a native implementation of the RDP naive Bayesian classifier.

AuthorBenjamin Callahan <benjamin.j.callahan@gmail.com>, Paul McMurdie, Susan Holmes
Bioconductor views Classification Metagenomics Microbiome Sequencing
Date of publicationNone
MaintainerBenjamin Callahan <benjamin.j.callahan@gmail.com>
LicenseLGPL-3
Version1.4.0
URL http://benjjneb.github.io/dada2/
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("dada2")

Getting started

Package overview
README.md
Introduction to dada2

Popular man pages

fastqFilter: Filter and trim a fastq file.
fastqPairedFilter: Filters and trims paired forward and reverse fastq files.
learnErrors: Learns the error rates from an input list, or vector, of file...
mergePairs: Merge denoised forward and reverse reads.
mergeSequenceTables: Merge two or more sample-by-sequence observation matrices.
plotQualityProfile: Plot quality profile of a fastq file.
uniquesToFasta: Write a uniques vector to a FASTA file
See all...

All man pages Function index File listing

Man pages

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...
dada: High resolution sample inference from amplicon data.
dada2-package: DADA2 package
dada-class: The object class returned by 'dada'
dada_to_seq_table: Map denoised sequence to each read.
derep-class: A class representing dereplicated sequences
derepFasta: derepFasta creates a derep-class object from a fasta file, by...
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...
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.
getFasta: Read a FASTA file into a named uppercase character vector.
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...
isBimera: Determine if input sequence is a bimera of putative parent...
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...
learnErrors: Learns the error rates from an input list, or vector, of file...
loessErrfun: Use a loess fit to estimate error rates from transition...
makeSequenceTable: Construct a sample-by-sequence observation matrix.
makeSpeciesFasta_RDP: This function creates the dada2 assignSpecies fasta file for...
makeSpeciesFasta_Silva: This function creates the dada2 assignSpecies fasta file for...
mergePairs: Merge denoised forward and reverse reads.
mergePairsByID: Merge forward and reverse reads after DADA denoising, even if...
mergeSequenceTables: Merge two or more sample-by-sequence observation matrices.
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.
qtables2: Internal tables function
removeBimeraDenovo: Remove bimeras from collections of unique sequences.
setDadaOpt: Set DADA options
show-methods: method extensions to show for dada2 objects.
tperr1: An empirical error matrix.
uniquesToFasta: Write a uniques vector to a FASTA file
uniques-vector: The named integer vector format used to represent collections...

Functions

C_assign_taxonomy Source code
C_assign_taxonomy2 Source code
C_eval_pair Source code
C_isACGT Source code
C_is_bimera Source code
C_matchRef Source code
C_matrixEE Source code
C_nwalign Source code
C_nwvec Source code
C_pair_consensus Source code
C_subpos Source code
C_table_bimera2 Source code
addSpecies Man page Source code
assignSpecies Man page Source code
assignTaxonomy Man page Source code
c,dada-method Man page
c,derep-method Man page
checkConvergence Source code
collapseNoMismatch Man page Source code
combineDereps2 Source code
dada Man page Source code
dada-class Man page
dada2-package Man page
dada_to_seq_table Man page Source code
dada_uniques Source code
derep-class Man page
derepFasta Man page Source code
derepFastq Man page Source code
errBalancedF Man page
errBalancedR Man page
errExtremeF Man page
errExtremeR Man page
errHmpF Man page
errHmpR Man page
evaluate_kmers Man page Source code
fastqFilter Man page Source code
fastqPairedFilter Man page Source code
filterAndTrim Man page Source code
getAbund Source code
getBadBases Source code
getDadaOpt Man page Source code
getErrors Man page Source code
getFasta Man page Source code
getNseq Source code
getSequences Man page Source code
getUniques Man page Source code
inflateErr Man page Source code
is.list.of Source code
is.sequence.table Source code
isBadBaseFP Source code
isBimera Man page Source code
isBimeraDenovo Man page Source code
isBimeraDenovoTable Man page Source code
isMatch Source code
isPhiX Man page Source code
isShift Source code
isShiftDenovo Man page Source code
isShiftedPair Source code
learnErrors Man page Source code
loessErrfun Man page Source code
makeSequenceTable Man page Source code
makeSpeciesFasta_RDP Man page Source code
makeSpeciesFasta_Silva Man page Source code
mapHits Source code
matchGenera Source code
mergePairs Man page Source code
mergePairsByID Man page Source code
mergeSequenceTables Man page Source code
names<-,dada,ANY-method Man page
names<-,derep,ANY-method Man page
nwalign Man page Source code
nwextract Source code
nwhamming Man page
pfasta Source code
plotComplementarySubstitutions Man page Source code
plotErrors Man page Source code
plotQualityProfile Man page Source code
qtables2 Man page Source code
rc Source code
removeBimeraDenovo Man page Source code
sameOrder Source code
setDadaOpt Man page Source code
show,dada-method Man page
show,derep-method Man page
strdiff Source code
tperr1 Man page
uniques-vector Man page
uniquesToFasta Man page Source code

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/RcppExports.R
R/allClasses.R
R/allPackage.R
R/chimeras.R
R/dada.R
R/errorModels.R
R/filter.R
R/misc.R
R/multiSample.R
R/paired.R
R/plot-methods.R
R/sequenceIO.R
R/show-methods.R
R/taxonomy.R
README.md
build
build/vignette.rds
data
data/errBalancedF.rda
data/errBalancedR.rda
data/errExtremeF.rda
data/errExtremeR.rda
data/errHmpF.rda
data/errHmpR.rda
data/tperr1.rda
inst
inst/CITATION
inst/NEWS
inst/doc
inst/doc/dada2-intro.R
inst/doc/dada2-intro.Rmd
inst/doc/dada2-intro.html
inst/extdata
inst/extdata/phix_genome.fa
inst/extdata/sam1F.fastq.gz
inst/extdata/sam1R.fastq.gz
inst/extdata/sam2F.fastq.gz
inst/extdata/sam2R.fastq.gz
inst/include
inst/include/dada2.h
inst/include/dada2_RcppExports.h
man
man/addSpecies.Rd
man/assignSpecies.Rd
man/assignTaxonomy.Rd
man/collapseNoMismatch.Rd
man/dada-class.Rd
man/dada.Rd
man/dada2-package.Rd
man/dada_to_seq_table.Rd
man/derep-class.Rd
man/derepFasta.Rd
man/derepFastq.Rd
man/errBalancedF.Rd
man/errBalancedR.Rd
man/errExtremeF.Rd
man/errExtremeR.Rd
man/errHmpF.Rd
man/errHmpR.Rd
man/evaluate_kmers.Rd
man/fastqFilter.Rd
man/fastqPairedFilter.Rd
man/filterAndTrim.Rd
man/getDadaOpt.Rd
man/getErrors.Rd
man/getFasta.Rd
man/getSequences.Rd
man/getUniques.Rd
man/inflateErr.Rd
man/isBimera.Rd
man/isBimeraDenovo.Rd
man/isBimeraDenovoTable.Rd
man/isPhiX.Rd
man/isShiftDenovo.Rd
man/learnErrors.Rd
man/loessErrfun.Rd
man/makeSequenceTable.Rd
man/makeSpeciesFasta_RDP.Rd
man/makeSpeciesFasta_Silva.Rd
man/mergePairs.Rd
man/mergePairsByID.Rd
man/mergeSequenceTables.Rd
man/nwalign.Rd
man/nwhamming.Rd
man/plotComplementarySubstitutions.Rd
man/plotErrors.Rd
man/plotQualityProfile.Rd
man/qtables2.Rd
man/removeBimeraDenovo.Rd
man/setDadaOpt.Rd
man/show-methods.Rd
man/tperr1.Rd
man/uniques-vector.Rd
man/uniquesToFasta.Rd
src
src/Makevars
src/RcppExports.cpp
src/Rmain.cpp
src/chimera.cpp
src/cluster.cpp
src/dada.h
src/error.cpp
src/evaluate.cpp
src/filter.cpp
src/misc.cpp
src/nwalign_endsfree.cpp
src/nwalign_vectorized.cpp
src/pval.cpp
src/strmap.cpp
src/strmap.h
src/taxonomy.cpp
vignettes
vignettes/Clearness.css
vignettes/dada2-intro.Rmd
dada2 documentation built on May 20, 2017, 9:15 p.m.

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