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Divisive Amplicon Denoising Algorithm DADA

Corrects amplicon errors without constructing Operational Taxonomic Units (OTUs). DADA2 is an R package that implements a quality-aware model of Illumina amplicon errors. This application is reference-free, and applicable to any genetic locus. It also implements the full amplicon workflow: filtering, dereplication, chimera identification, and merging paired-end reads. It enhances the study of microbial communities by allowing researchers to accurately reconstruct amplicon-sequenced communities at the highest resolution.

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DADA versioning

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DADA classification

  • Eubacteria
    • Bacillus subtilis
    • Escherichia coli
    • Mycobacterium tuberculosis
    • Mycoplasma pneumoniae
    • Helicobacter pylori
    • Staphylococcus aureus

DADA specifications

Software type:
Package/Module
Restrictions to use:
None
Input format:
FASTQ
Operating system:
Unix/Linux
License:
GNU Lesser General Public License version 3.0
Version:
1.5.2
Stability:
Stable
Maintained:
Yes
Interface:
Command line interface
Input data:
Amplicon sequencing data.
Biological technology:
Illumina
Programming languages:
R
Computer skills:
Advanced
First release date:
2016
Conda:
https://bioconda.github.io/recipes/bioconductor-dada2/README.htm

DADA support

Documentation

Maintainer

  • Benjamin Callahan <>

Additional information

Previous version: https://github.com/mjrosen/dadahttp://benjjneb.github.io/dada2/

Credits

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Publications

Institution(s)

Department of Statistics, Stanford University, Stanford, CA, USA; Second Genome, South San Francisco, CA, USA; Department of Applied Physics, Stanford University, Stanford, CA, USA

Funding source(s)

Supported by the NSF (DMS-1162538), the NIH (R01AI112401) and the Samarth Foundation (Stanford Microbiome Seed Grant).

Link to literature

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