Russ Corbett-Detig @russcd.bsky.social · 27/08/2026Hard to beat days when I have time to walk/hike home. 051 0
Russ Corbett-Detig @russcd.bsky.social · 31/03/2026eDNA is possibly the coolest application! Below: read-level placement across a pan-vertebrate mitochondrial pangenome (left) where a clear cluster of read assignments supports the presence of many mammoth reads (right). Processing ~9 billion reads took just 8 minutes! 0135 0
Russ Corbett-Detig @russcd.bsky.social · 31/03/2026Even in complex mixtures, Panmap does a really good job of sorting out their identities and relative contributions to the sample. 130 0
Russ Corbett-Detig @russcd.bsky.social · 31/03/2026Panmap can also evaluate sample mixtures (e.g., what you get from wastewater or eDNA), by scoring the reads separately against every node and then estimating the abundances of lineages via EM. 110 0
Russ Corbett-Detig @russcd.bsky.social · 31/03/2026Because we score placements dynamically during a single tree traversal, it is very fast. Panmap takes less than one second to place a SARS-CoV-2 sample onto a 20,000 sample phylogeny, align the read, and call genotypes. 110 0
Russ Corbett-Detig @russcd.bsky.social · 31/03/2026Panmap gets really accurate placements, even at very low sequencing depths. 110 0
Russ Corbett-Detig @russcd.bsky.social · 31/03/2026There is a ton of cool stuff you can do using the index. In the first application, Panmap place a single sample onto the tree *without assembly* using the raw reads and then can align and genotype based on this closest known relative. 120 0
Russ Corbett-Detig @russcd.bsky.social · 31/03/2026The central innovation of Panmap is indexing PanMANs by producing a “syncmer annotated tree”, where seed edits are stored only where sequences on the phylogeny change (including inferred ancestors). The index therefore exploits a type of “phylogenetic compression” and is very compact. 120 0
Russ Corbett-Detig @russcd.bsky.social · 03/03/2026Thanks so much, Ian! This means a lot coming from a mighty core-pivotal 17. 110 0
Russ Corbett-Detig @russcd.bsky.social · 24/02/2026@pratikkatte.bsky.social and I just released Lorax 🌲, a tool for interactive exploration of biobank-scale ancestral recombination graphs (ARGs). If you’ve ever wanted to scroll across the ancestries of thousands of genomes… this is for you. 25228 0
