GRUNWALDLAB . GITHUB . IO {
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Title:
Simultaneous Analysis of Multiplexed Metabarcodes • demulticoder
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>.
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Keywords {🔍}
cutadapt, package, demulticoder, metabarcodes, install, data, files, author, version, dada, terminal, window, cran, test, srfastqgz, overwriteexisting, true, sudermann, foster, dawson, phan, chang, grünwald, documentation, analysis, multiplexed, commands, input, installation, instructions, change, make, loaded, directory, set, check, output, source, code, martha, zachary, samantha, hung, jeff, niklaus, license, started, main, simultaneous, metabarcoding,
Topics {✒️}
org/packages/release/bioc/html/phyloseq org/packages/release/bioc/html/dada2 io/en/stable/installation /grunwaldlab/demulticoder/ citation convert asv matrix analyze data derived test directory located trim reads user bug fixes /usr/bin/cutadapt oomycetes supported metabarcodes install cutadapt program sudermann author multiplexed metabarcodes introduction cutadapt cutadapt --version samantha dawson copyright holder zachary hung phan dada2 wrapper package cutadapt installation instructions martha sudermann niklaus grünwald html phyloseq data set format databases file jeff chang input directory source code dawson scl io/demulticoder/ terminal window zachary foster foster zsl grünwald nj metabarcodes multiplexed multiplexed metabarcodes input files simultaneous analysis unique metabarcode martha html metacoder multiple metabarcodes main commands contents demulticoder 0 grunwaldlab/demulticoder chang jh latest version development version abridged version
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