Simultaneous Analysis of Multiplexed Metabarcodes
Assign taxonomy functions
Assign taxonomy
Combine taxonomic assignments and bootstrap values for each metabarcod...
Filter ASV abundance matrix and convert to 'taxmap' and 'phyloseq' obj...
Count overlap to see how well the reads were merged
Make ASV sequence matrix
Main command to trim primers using 'Cutadapt' and core 'DADA2' functio...
Wrapper function for filterAndTrim function from 'DADA2', to be used...
Format ASV abundance matrix
General functions to format user-specified databases
An 16S database that has modified headers and is output in the referen...
An ITS database that has modified headers and is output in the referen...
An other, user-specified database that is initially in the format spec...
An second user-specified database that is initially in the format spec...
Create modified reference rps10 database for downstream analysis
Retrieve the paths of the filtered and trimmed Fastq files
Get primer counts for reach sample after primer removal and trimming s...
Get primer counts for reach sample before primer removal and trimming ...
Final inventory of read counts after each step from input to removal o...
Function to infer ASVs, for multiple loci
Core 'DADA2' function to learn errors and infer ASVs
Quality filtering to remove chimeras and short sequences
Make an amplified sequence variant (ASV) abundance matrix for each of ...
Prepare for primmer trimming with 'Cutadapt'. Make new sub-directories...
Plots a histogram of read length counts of all sequences within the AS...
Merge forward and reverse reads
Take in user's forward and reverse sequences and creates the complemen...
Wrapper script for plotQualityProfile after trim steps and primer remo...
Wrapper function for plotQualityProfile function
Prepare final ASV abundance matrix
Read metadata file from user and combine and reformat it, given primer...
Prepare reads for primer trimming using 'Cutadapt'
Matching Order Primer Check
Run 'DADA2' taxonomy functions for single metabarcode
Takes in the FASTQ files from the user and creates a data.frame with...
Take in user's 'DADA2' parameters and make a data frame for downstream...
A function for calling read_fastq, primer_check, and remove_ns functio...
Wrapper function for core 'DADA2' filter and trim function for first f...
Core function for running 'Cutadapt'
Set up directory paths for subsequent analyses
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>.
Useful links