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DADA specifications

Information


Unique identifier OMICS_01117
Name DADA
Alternative name Divisive Amplicon Denoising Algorithm
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data Amplicon sequencing data.
Input format FASTQ
Biological technology Illumina
Operating system Unix/Linux
Programming languages C, MATLAB, Perl
License GNU Lesser General Public License version 3.0
Computer skills Advanced
Stability Stable
Maintained Yes

Taxon


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

Download


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Versioning


No version available

Maintainers


  • person_outline Benjamin Callahan
  • person_outline Michael Rosen

Additional information


https://github.com/mjrosen/dada

Publication for Divisive Amplicon Denoising Algorithm

DADA citations

 (6)
library_books

Human Microbiome Acquisition and Bioinformatic Challenges in Metagenomic Studies

2018
Int J Mol Sci
PMCID: 5855605
PMID: 29382070
DOI: 10.3390/ijms19020383

[…] operation may affect real phylogenetic diversity, because very similar taxa may be not correctly discriminated. Consequently, alternative strategies, namely sub-OTUs methods, are becoming available. Divisive Amplicon Denoising Algorithm 2 (DADA2) is an open-source algorithm implemented in R, which uses a statistical inference to correct amplicon errors []. This package includes all the analytical […]

library_books

Comparing the Healthy Nose and Nasopharynx Microbiota Reveals Continuity As Well As Niche Specificity

2017
Front Microbiol
PMCID: 5712567
PMID: 29238339
DOI: 10.3389/fmicb.2017.02372

[…] of high-quality sequences produced by modern sequencing technologies, such as Illumina MiSeq (reviewed in ). Therefore, alternative algorithms that detect more fine-scale variations like MED (, ) and Divisive Amplicon Denoising Algorithm 2 (DADA2) () have recently emerged, resulting in improved precision of diversity and dissimilarity measures. Since both the nose and the nasopharynx are low-compl […]

library_books

First Insights into the Diverse Human Archaeome: Specific Detection of Archaea in the Gastrointestinal Tract, Lung, and Nose and on Skin

2017
MBio
PMCID: 5686531
PMID: 29138298
DOI: 10.1128/mBio.00824-17

[…] , we focused on optimal primer selection and analyzed the ability of available NGS sequence processing pipelines, namely mothur (), QIIME (Quantitative Insights Into Microbial Ecology) (), and DADA2 (Divisive Amplicon Denoising Algorithm) (), to expand the picture of the human archaeome.More specifically, we present two main approaches. We first used a PCR-based detection method to determine the p […]

library_books

Analysing Microbial Community Composition through Amplicon Sequencing: From Sampling to Hypothesis Testing

2017
Front Microbiol
PMCID: 5591341
PMID: 28928718
DOI: 10.3389/fmicb.2017.01561

[…] ly meaningful OTU independently of a predefined level of similarity. Each of them has a different strategy to separate the noise introduced by PCR and sequencing from true biological diversity.DADA2 (Divisive Amplicon Denoising Algorithm 2) initially divides amplicons by considering their abundance distribution (since common reads are more likely to be true sequences) and sequence distance from ot […]

library_books

Analytical Tools and Databases for Metagenomics in the Next Generation Sequencing Era

2013
PMCID: 3794082
PMID: 24124405
DOI: 10.5808/GI.2013.11.3.102

[…] ences by retaining representative reads. Several denoising algorithms have been suggested so far. PyroNoise [] implements a flowgram clustering method, and other denoising tools, such as Denoiser [], DADA [], and Acacia [], use sequence abundance information on the denoising process. Similarly, single-linkage preclustering can be used before performing the formal OTU clustering to reduce 'noise' s […]

library_books

Fungal community analysis by high throughput sequencing of amplified markers – a user's guide

2013
New Phytol
PMCID: 3712477
PMID: 23534863
DOI: 10.1111/nph.12243

[…] pplied by the sequencing factory is at best a poor replacement for sequence quality management programs such as ampliconnoise (Quince et al., ), the Denoiser implemented in qiime (Reeder & Knight, ), dada (Rosen et al., ) and acacia (Bragg et al., ), which are all tailored for high-throughput sequencing data. ampliconnoise also supports detection of sequence chimeras, whose presence otherwise woul […]

Citations

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

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