dada2
Bioc currentAccurate, high-resolution sample inference from amplicon sequencing data
Release Lineage
Entered 3.3 · May 4, 2016
Current · Requires R 4.6
Description
The dada2 package infers exact amplicon sequence variants (ASVs) from high-throughput amplicon sequencing data, replacing the coarser and less accurate OTU clustering approach. The dada2 pipeline takes as input 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, and species-level assignment to 16S rRNA gene fragments by exact matching.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
188 37 exported
Complexity
8.7 avg / 95 max
Call network
188 nodes / 208 edges
Test coverage is not measured for Bioconductor packages; nodes fall back to a neutral fill.
Call graph
Open call graph →Lowest coverage
Per-function coverage is not measured for this package yet.
Code
Structure
Lines of code
13,507
Files
115
Compiled share
33.6%
Has compiled src
Yes
Language breakdown
API
Exported functions
38
Internal functions
50
Recent export changes
Testing
Has tests
No
Test-to-code ratio
0.00
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
0%
Unsafe pattern score
0
Dep constraint coverage
100%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
3.4.0
System requirements
1 externalGNU make
C++ standard
C++11
License
LGPL-2
License flags
SPDX valid, OSI approved
History
Versions
21
First release
2016-05-22
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
100%
Dep drift
7
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 58 (7 internal)includes a package overview page
- Examples that run
- 97%37 run in a plain check · 1 never run
- Exported functions with examples
- 100%
- Documented parameters
- 100%
- Return-value docs
- 100%
- Help pages citing references
- 0%
Repository practices
2 development-tooling and community-health practices detected across 2 families in the upstream repository
Checks run against github.com/benjjneb/dada2 on 2026-10-22.
GitHub Pages site last deployed 2025-12-15
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| errBalancedF | matrix | 16 × 41 | No other package |
| errBalancedR | matrix | 16 × 41 | No other package |
| tperr1 | matrix | 16 × 41 | No other package |
Topics
Depended on by (5)
Bioconductor (1)
CRAN (4)
Suggested by (3)
People (from the free-text Author field)
Cite
Cite this package
Run in R for the authors' entry:
citation("dada2")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1038/nmeth.3869.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.