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

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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.

Author
Benjamin Callahan <benjamin.j.callahan@gmail.com>, Paul McMurdie, Susan Holmes
Date of publication
None
Maintainer
Benjamin Callahan <benjamin.j.callahan@gmail.com>
License
LGPL-3
Version
1.2.0
URLs

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