Feather mite genomics experiment

Alix Matthews

Associated manuscript: https://doi.org/10.3390/life13102054

As a general overview, this project aims to compare the sequencing efficiency and population genetics of an experimental set of feather mite samples (1 mite vs. 5 mites vs. 20 mites in a single extraction - each from the same feather - of Amerodectes protonotaria).

Files needed at various steps:

• These may or may not be in the subdirectories
• 20210816_exp_filenames.txt: all files, for the initial PP steps; used in 00_PP_20210903 steps
• 20210816_exp_filenames_PROW953_only.txt: only PROW953R1, which had a lot of contamination; used in 01_aTRAM_COI_20220901 step
• 20210816_exp_filenames_SNPpipeline.txt: all samples, just added an extra useful column, used in 04_SNP_20221013 steps
• 20210816_exp_filenames_SNPpipeline_PROW953_only.txt: only PROW953R1, which had a lot of contamination; used in 01_RemoveBacteria_20220901 steps

Directories below and order of operations

00_PP_20210903

Initial pre-processing steps for the experimental samples (n=12). These are high in GC content, so will probably have to do several passes of pre-processing. This is a "standard" initial pre-processing.

01_aTRAM_COI_20220826

Making sure all samples are A. protonotaria ... but had issue with one (PROW953R1), so had to do a few more extra steps

01_RemoveBacteria_20220901

Removing bacteria reads from PROW953R1 and compare mapping rates

01_aTRAM_COI_20220901

Redoing aTRAM (COI) on all samples

03_IndexRef

Indexing the reference (NCBI deposited genome)

04_SNP_20221013

SNP pipeline for all samples

05_final-analysis-files

All files needed for the FINAL analyses. Lots of intermediate/unused files exist (in my other private repo, alixmatthews/20210816_projects/20210816_exp), but not in this cleaned up repo :)

final_figures

Final figures used in publication