156 - Ancient problems require ancient solutions - part 2
from Micro binfie podcast Hosted by Microbial Bioinformatics
In Part 2 of Ancient problems require ancient solutions, host Nabil Ali Khan brings James Fellows Yates back to the mic to go deeper into how ancient metagenomics actually gets done. They dig into dental calculus — mineralised plaque whose bone-like hydroxyapatite locks DNA in place for tens of thousands of years (James recovered a microbiome from a 100,000-year-old Neanderthal), what it tells us about diet, dysbiosis and the rise of dental disease after the Neolithic, and even a coming paper on a famous historical Briton with the highest ancient-DNA yield ever seen from calculus. Then it's onto the tooling: the origin story of nf-core/eager, why ancient DNA still needs a 10-year-deprecated GATK unified genotyper, the birth of the now-ubiquitous nf-core Metro-Map pipeline diagrams, and how James and the SPAAM community wrote the open textbook Introduction to Ancient Metagenomics as a practical guide for anyone — bioinformatician or historian — walking into the field. Guest: James Fellows Yates Hosts: Dr Nabil Ali Khan, Dr Lee Katz, Prof Andrew Page Introduction to Ancient Metagenomics (open textbook) — https://www.spaam-community.org/intro-to-ancient-metagenomics-book/ SPAAM community — https://spaam-community.org nf-core/eager — https://nf-co.re/eager AncientMetagenomeDir — https://github.com/SPAAM-community/AncientMetagenomeDir AMDirT — https://github.com/SPAAM-community/AMDirT nf-core Metro-Map guide — https://nf-co.re/docs/contributing/tutorials/creating_with_nf_core_tools#metro-map
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