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...

Files in this package

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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