benjjneb/dada2: Accurate, high-resolution sample inference from amplicon sequencing data
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.
Getting started
Browse package contents
Package details |
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| Author | Benjamin Callahan <benjamin.j.callahan@gmail.com>, Paul McMurdie, Susan Holmes |
| Bioconductor views | Classification ImmunoOncology Metagenomics Microbiome Sequencing |
| Maintainer | Benjamin Callahan <benjamin.j.callahan@gmail.com> |
| License | LGPL-2 |
| Version | 1.31.0 |
| URL | http://benjjneb.github.io/dada2/ |
| Package repository | View on GitHub |
| Installation |
Install the latest version of this package by entering the following in R:
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