snpArcher

<img src="./docs/img/logo.png" alt="snpArcher logo" height="300"/>

03/30/2026: We suggest using Snakemake v9.12 due to a regression with resource parsing.

snpArcher is a reproducible workflow optimized for nonmodel organisms and comparisons across datasets, built on the Snakemake workflow management system. It provides a streamlined approach to dataset acquisition, variant calling, quality control, and downstream analysis.

Usage

For usage instructions and complete documentation, please visit our docs.

Datasets generated by snpArcher

A number of resequencing datasets have been run with snpArcher generating consistent variant calls, available via Globus in the Comparative Population Genomics Data collection. Details of data processing are described in our manuscript. If you use any of these datasets in your projects, please cite both the snpArcher paper and the original data producers.

Citing snpArcher

• Cade D Mirchandani, Allison J Shultz, Gregg W C Thomas, Sara J Smith, Mara Baylis, Brian Arnold, Russ Corbett-Detig, Erik Enbody, Timothy B Sackton, A fast, reproducible, high-throughput variant calling workflow for population genomics, Molecular Biology and Evolution, 2023;, msad270, https://doi.org/10.1093/molbev/msad270

• Also, make sure to cite the tools you used within snpArcher.