Please cite the paper if any of this was useful to you. This work was made possible by our Māori partners at the East Otago Taiāpure. Please ensure you are properly consulting if requesting the data from the Aotearoa Genomics Data Repository.
Please consider using the files in the order of:
CutAdapt_F/R_Barcodes - to help demultiplex the data 2-4_data_analyzing_final_script.sh - to demultiplex, merge, filter, and put the data into an OTU table Note that 1_CutAdaptDemux.sh and 3_filt+unoise.sh scripts can be modified and combined for the above script
DataMunge-eDNAamplicon.R reads in the OTU table (Paua.eDNA.ee10.csv) and makes some changes for readability and labeling. eDNA-Paua-Graphs.R helps to create graphs for the paper.
Haplotype Accumulation graph and Maps are stand-alone. To analyze mitochondrial tissue samples, the Eager Pipeline was used and can be referred to here: https://nf-co.re/eager or https://github.com/nf-core/eager