2.2.5.1 Counts table generation
Nucleotide- and amino acid-based counts tables are generated within the Analyze pipeline. Counts tables for ASVs and ncASVs are produced using the VSEARCH program and the USEARCH algorithm (Edgar, 2010). Optionally, users can replace the use of the USEARCH algorithm with the use of the “–search_exact” feature provided by VSEARCH for exact ASV counts tables (Rognes et al., 2016). The aminotype and pcASV counts tables are generated by aligning translated merged reads to reference amino acid sequences with DIAMOND blastx (Buchfink et al., 2015). Sequence abundance information (in a comma delimited counts table) is then generated with a custom BASH script, which quantifies the number of alignments to each reference aminotype or pcASV from the DIAMOND output file. Users have the option to edit and adjust option parameters for the VSEARCH and DIAMOND counts table generation processes within the configuration file. All count files are stored in the results directory and are processed and visualized within Analyze reports as relative abundance bar plots.