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dada2

Exact sample inference from Illumina amplicon data. Resolves real variants differing by as little as one nucleotide.

DADA2 Articles

Preprint describing DADA2's accuracy and precision: DADA2: High resolution sample inference from amplicon data

Peer reviewed publication: In progress.

Installation

source("https://bioconductor.org/biocLite.R")
biocLite("dada2")

Tutorial

A walkthrough of the DADA2 pipeline for paired end Illumina Miseq data is available on the DADA2 front page.

Other Resources

Planned feature improvements are publicly catalogued at the main DADA2 development site on github; specifically on the "Issues" page for DADA2:

https://github.com/benjjneb/dada2/issues

If the feature you are hoping for is not listed, you are welcome to add it as a feature request "issue" on this page. This request will be publicly available and listed on the page.

Bugs and difficulties in using DADA2 are also welcome on the issue tracker.

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Version

Version

1.0.3

License

LGPL-3

Maintainer

Benjamin Callahan

Last Published

February 15th, 2017

Functions in dada2 (1.0.3)

assignTaxonomy

Classifies sequences against reference training dataset.
errExtremeR

An empirical error matrix.
errBalancedR

An empirical error matrix.
dada_to_seq_table

Map denoised sequence to each read.
mergePairsByID

Merge forward and reverse reads after DADA denoising, even if reads were not originally ordered together.
loessErrfun

Use a loess fit to estimate error rates from transition counts.
tperr1

An empirical error matrix.
inflateErr

Inflates an error rate matrix by a specified factor, while accounting for saturation.
getDadaOpt

Get DADA options
qtables2

Internal tables function
errHmpF

An empirical error matrix.
plotErrors

Plot observed error rates after denoising.
plotQualityProfile

Plot quality profile of a fastq file.
uniques-vector

The named integer vector format used to represent collections of unique DNA sequences.
show,derep-method

method extensions to show for dada2 objects.
collapseNoMismatch

Combine together sequences that are identical up to shifts and/or length.
errBalancedF

An empirical error matrix.
isShiftDenovo

Identify sequences that are identical to a more abundant sequence up to an overall shift.
getSequences

Get vector of sequences from input object.
derep-class

A class representing dereplicated sequences
isBimera

Determine if input sequence is a bimera of putative parent sequences.
errExtremeF

An empirical error matrix.
derepFastq

Read in and dereplicate a fastq file.
dada-class

The object class returned by dada
uniquesToFasta

Write a uniques vector to a FASTA file
nwalign

Needlman-Wunsch alignment.
nwhamming

Hamming distance after Needlman-Wunsch alignment.
isBimeraDenovo

Identify bimeras from collections of unique sequences.
fastqFilter

Filter and trim a fastq file.
dada

High resolution sample inference from amplicon data.
evaluate_kmers

Generate the kmer-distance and the alignment distance from the given set of sequences.
isPhiX

Determine if input sequence(s) match the phiX genome.
fastqPairedFilter

Filters and trims paired forward and reverse fastq files.
errHmpR

An empirical error matrix.
setDadaOpt

Set DADA options
removeBimeraDenovo

Remove bimeras from collections of unique sequences.
dada2-package

DADA2 package
makeSequenceTable

Construct a sample-by-sequence observation matrix.
mergePairs

Merge denoised forward and reverse reads.
plotComplementarySubstitutions

Plot Substitution Pairs from DADA Result
getUniques

Get the uniques-vector from the input object.