Gombe noninvasive genomics

This repository contains the code used in Ozga, Webster, et al. to investigate the promise of various sources of noninvasively collected DNA in primate genomics.

For questions, contact: Tim Webster, University of Utah

Citation

If you use any code in this repository, please cite our preprint:

Ozga AT, Webster TH, Gilby IC, Wilson MA, Nockerts RS, Wilson ML, Pusey AE, Li Y, Hahn BH, Stone AC. 2020. Urine as a high quality source of host genomic DNA from wild populations.

The manuscript has been submitted for peer-review and we'll update the citation when it's published.

Goals

We aim to explicitly test the success of DNA capture and next-generation sequencing using noninvasive sources of DNA from wild chimpanzees from Gombe National Park, Tanzania.

Samples

This project has 26 total samples from:

• 10 individuals
• 4 sources (urine, feces, dental calculus, dentin)
• 4 capture methods (human exome, PTS whole genome, human whole genome, shotgun)

For the capture methods:

• "human exome" ("Exome" below) uses iDT XGEN human exome baits
• "PTS_WG" are a custom whole genome MYBaits kit produced by Arbor Biosciences using Pan troglodytes schweinfurthii DNA
• "Human_WG" is a MYcroarray whole genome capture kit (Human Masai male DNA)
• "Shotgun" is shotgun sequencing without capture

Individual	Capture	Urine	Feces	Dental calculus	Dentin
7365	Exome	Y	Y	N	N
7365	PTS_WG	N	Y	N	N
7365	Human_WG	N	Y	N	N
7150	Exome	Y	Y	N	N
7150	PTS_WG	N	Y	N	N
7150	Human_WG	N	Y	N	N
7069	Exome	N	Y	N	N
7069	PTS_WG	N	Y	N	N
7069	Human_WG	N	Y	N	N
7057	Exome	N	N	Y	Y
7057	Human_WG	N	N	Y	N
7057	Shotgun	N	N	Y	N
7072	Exome	Y	N	N	N
7535	Exome	Y	N	N	N
7433	Exome	N	N	Y	N
7433	Human_WG	N	N	Y	N
7433	PTS_WG	N	N	Y	N
7650	Exome	Y	N	N	N
7507	Exome	Y	Y	N	N
7507	Human_WG	N	Y	N	N
7507	PTS_WG	N	Y	N	N
7323	Exome	Y	N	N	N