DADA2 ITS workflow - fungal metabarcoding data to ASV and OTU table

DADA2 workflow modified to use for fungal metabarcoding data. Metabarcoding targets barcodes for the identification of species and taxonomic groups. Prior to sequencing, DNA undergoes amplification, a process that replicates genetic material encompassing a barcode marker for species identification. In this context, the fungal barcode used is the Internal Transcribed Spacer (ITS). Hence, the primers were designed specifically for the amplification of the ITS regions, facilitating fungal data segregation for the DADA2 workflow. Although the DADA2 workflow (v.1.16) is primarily designed for bacterial data, it can be modified to handle fungal metabarcoding data. The output generated includes an ASV and/or OTU table, wherein the ASV table provides a detailed record of the frequency and taxonomic details of each exact amplicon sequence variant, and the OTU table includes the count of sequences observed for each taxonomic unit, across different samples.

The source code files, 'DADA2.R' (the DADA2 workflow), 'FunctionsDADA2.R' (a script including all functions used by the DADA2 workflow), and 'ASV2OTU.R' (a script to transform your ASV table, thee output of the DADA2 workflow to an OTU table), are located in the 'scr' directory. Please note that the 'data' directory contains a file with the primers used for the test data, and it is expected that users add their own data to this directory. The 'results' directory contains the output of the DADA2 workflow, including the ASV (Amplicon Sequence Variant) and OTU (Operational Taxonomic Unit) tables.