sourmash-plugin-repeat-robust-mutation-rate-estimators 0.1.0

sourmash plugin for repeat-robust mutation rate estimation (r_pp, r_pc, r_cc).

sourmash-plugin-repeat-robust-mutation-rate-estimators

sourmash is a tool for biological sequence analysis and comparisons.

This plugin implements repeat-robust substitution rate estimators r_pp, r_pc, and r_cc based on FracMinHash sketches, as described in:

Wu, H. and Medvedev, P. (2026). Repeat-robust estimation of substitution rates from k-mer sketches. bioRxiv. https://www.biorxiv.org/content/10.64898/2026.04.01.715966v1

Installation

Install sourmash, then install this plugin:

# Option 1:
conda install -c conda-forge -c bioconda sourmash
pip install sourmash-plugin-repeat-robust-mutation-rate-estimators

# Option 2:
pip install sourmash
pip install sourmash-plugin-repeat-robust-mutation-rate-estimators

Verify the plugin is recognized:

sourmash scripts

You should see sketch and mutation_rate listed under available plugin commands.

Usage

Background

The three estimators treat the two input sequences asymmetrically: we assume string t is mutated from string s.

If unsure which is s and which is t, use the longer sequence as s.

Each estimator requires a specific sketch mode:

Estimator	s sketch mode	t sketch mode
r_pp	standard	standard
r_pc	standard	multiplicity
r_cc	extended	multiplicity

In general, estimators that use more information achieve higher accuracy.

Step 1: Sketch your sequences

# For r_pp
sourmash scripts sketch s.fa --sketch-mode standard    -o s.sig -k 21 --scaled 1000
sourmash scripts sketch t.fa --sketch-mode standard    -o t.sig -k 21 --scaled 1000

# For r_pc
sourmash scripts sketch s.fa --sketch-mode standard    -o s.sig -k 21 --scaled 1000
sourmash scripts sketch t.fa --sketch-mode multiplicity -o t.sig -k 21 --scaled 1000

# For r_cc
sourmash scripts sketch s.fa --sketch-mode extended    -o s.sig -k 21 --scaled 1000
sourmash scripts sketch t.fa --sketch-mode multiplicity -o t.sig -k 21 --scaled 1000

Sketch modes:

• standard: stores distinct k-mer hashes and L, where L = |x| - k + 1 is the total number of k-mers in string x. Use as s or t for r_pp.
• multiplicity: stores k-mer hashes with per-hash counts and L. Use as t for r_pc and r_cc.
• extended: stores distinct k-mer hashes, L, and a precomputed correction constant sum_occ_h1. Use as s for r_cc. Note: computing sum_occ_h1 requires reading the full sequence and may take longer for large genomes.

Step 2: Estimate mutation rate

sourmash scripts mutation_rate --estimator r_pp --s-sig s.sig --t-sig t.sig
sourmash scripts mutation_rate --estimator r_pc --s-sig s.sig --t-sig t.sig
sourmash scripts mutation_rate --estimator r_cc --s-sig s.sig --t-sig t.sig

Example output:

Estimator : r_cc
k         : 21
scaled    : 1000
L_s       : 4800000
Estimated mutation rate : 0.012345

Support

Please file issues at https://github.com/Wu-Haonan/sourmash-plugin-repeat-robust-mutation-rate-estimators/issues

Dev docs

sourmash-plugin-repeat-robust-mutation-rate-estimators is developed at https://github.com/Wu-Haonan/sourmash-plugin-repeat-robust-mutation-rate-estimators.

Citation

If you use this plugin, please cite:

Wu, H. and Medvedev, P. (2026). Repeat-robust estimation of substitution rates
from k-mer sketches. bioRxiv.
https://www.biorxiv.org/content/10.64898/2026.04.01.715966v1

License

MIT License. See LICENSE for details.