CCavallo_Thesis Appendix_NGS Bioinformatics pipeline 18s.Rmd (13.93 kB)

CCavallo_Thesis Appendix_NGS Bioinformatics pipeline 18s.Rmd

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workflow
posted on 28.04.2020, 07:18 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

Funding

A top-down approach to ecosystem management using multivariate foraging strategies of an iconic marine top-predator

Australian Research Council

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