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.
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
117
Compiled share
33.6%
Has compiled src
Yes
Language breakdown
API
Exported functions
38
Internal functions
50
Recent export changes
Testing & CI
Has tests
No
Test-to-code ratio
0.00
testthat edition
–
CI present
Yes
CI type
["travis"]
PR gated
No
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
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
- Examples that run
- 97%
- Documented parameters
- 100%
- Return-value docs
- 100%
- References docs
- 0%
Topics
Depended on by (8)
CRAN (6)
People
Benjamin Callahan
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("dada2")Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-08-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.