Function reference

All functions

assign_tax()

Assign taxonomy functions

convert_asv_matrix_to_objs()

Filter ASV abundance matrix and convert to taxmap and phyloseq objects

cut_trim()

Main command to trim primers using Cutadapt and core DADA2 functions. If samples contain pooled barcodes, reads will also be demultiplexed

make_asv_abund_matrix()

Make an amplified sequence variant (ASV) abundance matrix This function generates an ASV abundance matrix using raw reads processed during previous steps, including read preparation, removing primers, and using DADA2 core denoising alogrithm to infer ASVs.

prepare_reads()

Prepare reads for primer trimming using Cutadapt