CCavallo_Thesis Appendix_NGS Bioinformatics pipeline 16S.Rmd

2020-04-28T07:15:59Z (GMT) by Cathy Cavallo
Bioinformatic workflow.
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:
* Removing
+ samples with less than 100 target reads
+ Non-target sequences
+ Specific samples (e.g. those that did not meet thresholds for inclusion, like CT)

* Producing group totals for higher taxonomic levels

* Calculating the frequency of occurrence (FOO) and relative read abundance (RRA) of items in the dataset