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Protocols

DADA2 specifications

Information


Unique identifier OMICS_30805
Name DADA2
Software type Package/Module
Interface Command line interface
Restrictions to use None
Biological technology Illumina
Operating system Unix/Linux, Mac OS, Windows
Programming languages C++, R
License GNU Lesser General Public License version 3.0
Computer skills Advanced
Version 1.8
Stability Stable
Maintained Yes

Download


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Versioning


No version available

Documentation


Maintainer


  • person_outline Benjamin Callahan

Additional information


http://benjjneb.github.io/dada2/tutorial.html

Publication for DADA2

DADA2 citations

 (54)
library_books

Multilevel social structure and diet shape the gut microbiota of the gelada monkey, the only grazing primate

2018
Microbiome
PMCID: 5935910
PMID: 29729671
DOI: 10.1186/s40168-018-0468-6

[…] ere predicted using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt 1.1.1) [] after normalizing for 16S rRNA gene copy number. Oligotyping was done using the DADA2 R-package [] with default parameters. DADA2 recognized 58,584 sequence variants, and for analysis of the data, the abundance table was filtered to retain only sequence variants that were observe […]

library_books

Comparing Microbiome Sampling Methods in a Wild Mammal: Fecal and Intestinal Samples Record Different Signals of Host Ecology, Evolution

2018
Front Microbiol
PMCID: 5938605
PMID: 29765359
DOI: 10.3389/fmicb.2018.00803

[…] aw reads across our 55 input libraries. We analyzed these metagenomic data using the open-source QIIME2 pipeline (Caporaso et al., ; Kuczynski et al., ). We first quality filtered sequences using the DADA2 algorithm (Callahan et al., ) as a QIIME2 plugin. DADA2 joins paired-end reads together, and then implements a quality-aware correcting model for amplicon data that denoises, removes chimeras an […]

library_books

Coral Bacterial Core Abundance and Network Complexity as Proxies for Anthropogenic Pollution

2018
Front Microbiol
PMCID: 5934943
PMID: 29755445
DOI: 10.3389/fmicb.2018.00833

[…] ta (). In brief, a total of 150,108 reads were obtained after demultiplexing with q2-DEMUX, with an average sequence length of 250 bp. The quality was filtered, replicated and chimera removed with q2-DADA2 (). Representative sequence sets for each DADA2 sequence variant were used for taxonomic classification.The remaining high-quality sequences were binned into operational taxonomic units (OTUs) a […]

library_books

SGLT2 inhibition via dapagliflozin improves generalized vascular dysfunction and alters the gut microbiota in type 2 diabetic mice

2018
PMCID: 5921754
PMID: 29703207
DOI: 10.1186/s12933-018-0708-x

[…] iSeq at the next-generation sequencing facility at Colorado State University. Paired-end sequence reads were concatenated and all combined 16 s sequences were filtered, trimmed and processed with the DADA2 (R bioconductor package []) implementation included in the open source bioinformatics tool myPhyloDB version 1.2.1 (http://www.myphylodb.org/). Briefly, all primers were removed from each sequen […]

library_books

Diversity, structure and sources of bacterial communities in earthworm cocoons

2018
Sci Rep
PMCID: 5919978
PMID: 29700426
DOI: 10.1038/s41598-018-25081-9

[…] fragment of the 16 S rRNA gene covering the V4 region by using a dual-index sequencing strategy and an Illumina MiSeq genome sequencer (Genomics Core Facility, Universitat Pompeu Fabra).The pipeline DADA2 (version 1.6) was used to infer the amplicon sequence variants (ASVs) present in each sample. Exact sequence variants provide a more accurate and reproducible description of amplicon-sequenced c […]

call_split

Do we treat our patients or rather periodontal microbes with adjunctive antibiotics in periodontal therapy? A 16S rDNA microbial community analysis

2018
PLoS One
PMCID: 5906003
PMID: 29668720
DOI: 10.1371/journal.pone.0195534
call_split See protocol

[…] of EMBL European Bioinformatics Institute under the study accession number PRJEB18651.Raw reads were then processed using the R language environment v.3.4.3 [] and RStudio v.1.0.153 [], following the DADA2 workflow described by Callahan et al. []. Reads were truncated (forward reads at position 260 and reverse reads at position 195 onwards) and filtered (maximum of 2 expected errors per read) on p […]

Citations

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DADA2 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
DADA2 funding source(s)
Supported by the NSF (DMS-1162538), the NIH (R01AI112401) and the Samarth Foundation (Stanford Microbiome Seed Grant).

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