CCavallo_Thesis Appendix_NGS Bioinformatics pipeline 18s.Rmd

Bioinformatic workflow.<div><div>This code will allow the user to clean and organise their DNA sample library and then calculate measures of taxon abundance for analysis. Important steps include: </div><div>* Removing </div><div> + samples with less than 100 target reads </div><div> + Non-target sequences </div><div> + Specific samples (e.g. those that did not meet thresholds for inclusion, like CT) </div><div><br></div><div>* Producing group totals for higher taxonomic levels </div><div><br></div><div>* Calculating the frequency of occurrence (FOO) and relative read abundance (RRA) of items in the dataset </div></div>