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demulticoder  

Simultaneous Analysis of Multiplexed Metabarcodes
View on CRAN: Click here


Download and install demulticoder package within the R console
Install from CRAN:
install.packages("demulticoder")

Install from Github:
library("remotes")
install_github("cran/demulticoder")

Install by package version:
library("remotes")
install_version("demulticoder", "0.1.2")



Attach the package and use:
library("demulticoder")
Maintained by
Martha A. Sudermann
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2025-05-05
Latest Update: 2025-05-05
Description:
A comprehensive set of wrapper functions for the analysis of multiplex metabarcode data. It includes robust wrappers for 'Cutadapt' and 'DADA2' to trim primers, filter reads, perform amplicon sequence variant (ASV) inference, and assign taxonomy. The package can handle single metabarcode datasets, datasets with two pooled metabarcodes, or multiple datasets simultaneously. The final output is a matrix per metabarcode, containing both ASV abundance data and associated taxonomic assignments. An optional function converts these matrices into 'phyloseq' and 'taxmap' objects. For more information on 'DADA2', including information on how DADA2 infers samples sequences, see Callahan et al. (2016) <doi:10.1038/nmeth.3869>. For more details on the demulticoder R package see Sudermann et al. (2025) <doi:10.1094/PHYTO-02-25-0043-FI>.
How to cite:
Martha A. Sudermann (2025). demulticoder: Simultaneous Analysis of Multiplexed Metabarcodes. R package version 0.1.2, https://cran.r-project.org/web/packages/demulticoder. Accessed 06 Aug. 2026.
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