Micro binfie podcast

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

What can DNA recovered from bones, teeth and paleofaeces tell us that living samples can't — and how do you keep modern contamination from drowning out a 1,000-year-old signal? In Part 1, host Nabil Ali Khan is joined by James Fellows Yates (bioinformatician, biomolecular archaeologist, and editor of the new open textbook Introduction to Ancient Metagenomics) for a tour of the field. They cover why ancient DNA arrives as 30–70 bp fragments with characteristic C→T "smiley plot" damage, how endogenous yields as low as 1% still count as a good sample, and the wet-lab lengths (bodysuits, UV, no kits) needed to keep libraries clean. They also dig into the big questions ancient microbial DNA is now answering — plague and TB origins, oral-microbiome loss since the Neolithic, AMR trends read from historical bear calculus — and how the SPAAM community, NF-core/eager and AncientMetagenomeDir grew up to support the work. Guest: James Fellows Yates Hosts: Dr Nabil Ali Khan, Dr Lee Katz, Prof Andrew Page SPAAM community — https://spaam-community.org nf-core/eager — https://nf-co.re/eager AncientMetagenomeDir — https://github.com/SPAAM-community/AncientMetagenomeDir Introduction to Ancient Metagenomics (open textbook) — https://www.spaam-community.org/intro-to-ancient-metagenomics-book/

Nabil, Andrew, and Lee talk with Liyang Diao and Valisha Shah from the nonprofit organization, Boston Women in Bioinformatics, a community that supports bioinformaticians in the Greater Boston area. We discuss the organization’s mission, the resources it provides, and what’s coming next for the group. boston-wib.org/

- Seebot https://github.com/happykhan/seebot - Ten quick tips to SNIFF out sustainable and secure scientific software | PLOS Computational Biology https://bsky.app/profile/stephenturner.us/post/3mqpkezwzls2m - Ten recommendations for creating usable bioinformatics command line software https://link.springer.com/article/10.1186/2047-217X-2-15

In this follow-up Software Deep Dive episode, we continue our conversation with Dr. Bede Constantinides (University of Birmingham) about the design and implementation of Deacon, a fast host-read removal tool for metagenomics. Deacon uses minimizers and k-mer set membership queries instead of alignment, allowing it to filter reads extremely quickly while balancing sensitivity and specificity. The tool is written in Rust, producing a small, fast binary and enabling very high throughput. We also discuss benchmarking with diverse viral and bacterial datasets, why tools like Kraken2 are not always ideal for host depletion, and why host read removal remains an unsolved problem—especially when balancing privacy, computational cost, and preservation of microbial reads. Links Deacon https://github.com/bede/deacon Hostile https://github.com/bede/hostile/ Bede Constantinides http://bede.im/ Kraken2 https://ccb.jhu.edu/software/kraken2/