Fig. 1

Schematic illustration of the BIOCOM-PIPE pipeline. The initial step in the analysis consists in checking uniqueness and preparing the files required to run the pipeline (light blue box). It is followed by a pre-processing step to check the quality of reads. Read pairs are demultiplexed if necessary, merged, and primers are trimmed (green box). The next key step consists in processing the clean reads by aligning them with a reference structure, hunting-recovering chimeras, clustering and post-clustering, and ending with diversity analysis (red box). The last step consists in generating a complete website providing all the results to be presented in tabular and graphics forms (purple box)