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

The dada2 package infers exact sequence variants (SVs) from amplicon data, replacing the commonly used and coarser OTU clustering approach. The dada2 pipeline inputs 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
Date of publicationNone
MaintainerBenjamin Callahan <benjamin.j.callahan@gmail.com>
LicenseLGPL-3
Version1.2.1
http://benjjneb.github.io/dada2/

View on Bioconductor

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.

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...

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...

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: 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.

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

addSpecies Man page
assignSpecies Man page
assignTaxonomy Man page
c,dada-method Man page
c,derep-method Man page
collapseNoMismatch Man page
dada Man page
dada2-package Man page
dada-class Man page
dada_to_seq_table Man page
derep-class Man page
derepFasta Man page
derepFastq Man page
errBalancedF Man page
errBalancedR Man page
errExtremeF Man page
errExtremeR Man page
errHmpF Man page
errHmpR Man page
evaluate_kmers Man page
fastqFilter Man page
fastqPairedFilter Man page
getDadaOpt Man page
getSequences Man page
getUniques Man page
inflateErr Man page
isBimera Man page
isBimeraDenovo Man page
isBimeraDenovoTable Man page
isPhiX Man page
isShiftDenovo Man page
loessErrfun Man page
makeSequenceTable Man page
makeSpeciesFasta_RDP Man page
makeSpeciesFasta_Silva Man page
mergePairs Man page
mergePairsByID Man page
mergeSequenceTables Man page
names<-,dada,ANY-method Man page
names<-,derep,ANY-method Man page
nwalign Man page
nwhamming Man page
plotComplementarySubstitutions Man page
plotErrors Man page
plotQualityProfile Man page
qtables2 Man page
removeBimeraDenovo Man page
setDadaOpt Man page
show,dada-method Man page
show,derep-method Man page
tperr1 Man page
uniquesToFasta Man page
uniques-vector Man page

Files

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

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