Fig. 1

Flowchart of the default MetaLAFFA workflow. The default MetaLAFFA workflow consists of three phases, quality control (top), read mapping (middle), and functional annotation (bottom). This flowchart outlines the individual processing steps taken in each phase (colored rectangular boxes), the intermediate outputs of these steps (grey rounded boxes), supporting data files required for specific steps (yellow rounded boxes), user-provided input to MetaLAFFA (red rounded box), and the final outputs of the pipeline (purple rounded boxes). Third-party tools used in the default pipeline workflow are indicated in parentheses for their associated processing steps. File types of all inputs, outputs, and supporting data files are indicated by file suffix