Micro binfie podcast

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/

In this Software Deep Dive episode, we talk with Dr. Bede Constantinides (University of Birmingham) about Deacon, a tool for removing host DNA reads from metagenomic datasets. We discuss why host read removal is a deceptively difficult problem, the limitations of alignment-based approaches, and how Deacon evolved from Bede's earlier tool Hostile. The conversation covers practical issues such as human contamination in metagenomes, balancing sensitivity vs specificity when filtering reads, and the computational challenges of working with large human reference datasets and pangenomes. This episode focuses on the background and motivation for Deacon. The next episode will dive deeper into how the method works. Links Deacon https://github.com/bede/deacon Hostile https://github.com/bede/hostile/ Bede Constantinides http://bede.im/ nf-core taxprofiler https://nf-co.re/taxprofiler Kraken2 https://ccb.jhu.edu/software/kraken2/