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December 13, 2021GeneticsOpen Access

Efficient ancestry and mutation simulation with msprime 1.0

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Authors

FBFranz BaumdickerGBGertjan BisschopDGDaniel Goldstein

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Overview

Computational study demonstrates rapid, memory-efficient ancestry and mutation simulation in population genetics, highlighting open-source improvements over specialized tools.

Key Points

  • To introduce msprime version 1.0, an open-source platform designed for rapid and memory-efficient ancestry and mutation simulation in population genetics.
  • Implemented algorithms for simulated ancestry and mutation generation based on the succinct tree sequence data structure and the tskit library.
  • Engineered the platform via a collaborative open-source development model with extensive testing and validation.
  • Benchmarked execution speed and memory efficiency against existing specialized population genetics simulation programs.
  • msprime 1.0 achieves execution speeds many times faster than specialized alternative simulation tools.
  • Memory efficiency is substantially improved relative to conventional software by using succinct tree sequences.

Cite This Study

Baumdicker et al. (2021) studied this question.

synapsesocial.com/papers/69d9614704deaa6ab568433dhttps://doi.org/10.1093/genetics/iyab229
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