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.