Tskit 1.0: a framework for efficient ARG analysis
Yan Wong, University of Oxford
November 11, 2025 | 15h00 | Hybrid Seminar (Zoom Link; Passcode: 111333)
Ancestral Recombination Graphs, or ARGs, a generalization of phylogenies with recombination, are becoming increasingly central to population genetics. I will outline the tskit software library for ARG storage and analysis, which permits integration of the popular msprime and SLiM simulators, and forms the backbone of the standard library of population genetic simulations (stdpopsim). Tskit is designed from the ground up to enable megascale genomics, providing efficient analysis tools for thousands or millions of whole genome sequences. Using examples from recent publications, I will showcase how tskit can be used for genetic analysis, as well as development of bespoke genetic algorithms, and how we are using it to infer genealogies from genome-scale data. I will conclude by discussing future plans and directions for tskit.
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