Pygenstrat: A Python package for EIGENSTRAT data processing
Dilek Koptekin
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Abstract
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Motivation: EIGENSTRAT format is widely used in ancient DNA population-genetic analyses but software for processing it is limited. pygenstrat is a Python command-line package that provides memory-efficient, chunked processing for large ancient-DNA EIGENSTRAT datasets and supports extensive filtering, subsetting, file updates, pseudo-haploidisation, allele polarisation, and conversion between text and binary formats. Results: Benchmarking versus convertf on the Allen Ancient DNA Resource (v62.0) reports 2–15× speedups and 90–95% memory reduction while producing equivalent outputs for standard operations. Availability: open-source (GitHub).
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