MetaWorks workflow to produce taxonomically assigned exact sequence variants.

To aid reproducibility, a Conda environment is provided. Although multiple Snakemake workflows are provided in MetaWorks, here we show the main workflow that generates taxonomically assigned ESVs. Input files are shown in the first panel (green), the ESV workflow is shown in the centre panel (blue), and outfiles are shown in the last panel (orange). The input files in white boxes are required by snakemake to run the appropriate workflow. The input files in green need to be supplied by the user. Note that only custom-trained classifiers such as for COI need to be supplied by the user whereas classifiers built-in to the RDP classifier are used automatically to process prokaryote 16S assignments, for example. The denoising step shown here includes the removal of rare clusters, sequences with putative errors, as well as chimeric sequences. The results are provided in a comma-separated value (CSV) file and shows each ESV per sample with read counts and taxonomic assignments. Abbreviations: Demultiplexed Illumina paired-end reads (R1 + R2), internal transcribed spacer (ITS) region, open reading frame sequences (ORFs).