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.
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-3 |
Version | 1.18.0 |
URL | http://benjjneb.github.io/dada2/ |
Package repository | View on Bioconductor |
Installation |
Install the latest version of this package by entering the following in R:
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