sketchlib 0.3.0

Genome and amino-acid sketching
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# sketchlib.rust <img src='sketchlib.rust_logo.png' align="right" height="139" />

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## Description

This is a reimplementation and extension of [pp-sketchlib](https://github.com/bacpop/pp-sketchlib)
in the rust language. This version is optimised for larger sample numbers, particularly
allowing subsets of samples to be compared.

v0.2.0 is the first stable release. We intend to keep the file format unchanged after this
point so sketch libraries will not need to be rebuilt.

## Documentation

See https://docs.rs/sketchlib

## Installation

Choose from:

1. Download a binary from the releases.
2. Use `cargo install sketchlib` or `cargo add sketchlib`.
3. Use conda install -c bioconda sketchlib.
4. Build from source

For 2) or 4) you must have the rust toolchain installed.

### OS X users

If you have an M1-4 (arm64) Mac, we aren't currently automatically building binaries, so would recommend either option 2) or 3) for best performance.

If you get a message saying the binary isn't signed by Apple and can't be run, use the following command to bypass this:

```
xattr -d "com.apple.quarantine" ./sketchlib
```

### Build from source

1. Clone the repository with git clone.
2. Run `cargo install --path .` or `RUSTFLAGS="-C target-cpu=native" cargo install --path .` to optimise for your machine.

## Citation

Please cite:

von Wachsmann J, Lorenz LJ, Russell MJ, Gurbich TA, Rodríguez-Bouza V, Horsfield ST, Lees JA, Finn RD (2026).\
Rapid and consistent clustering of millions of genomes highlights the diversity of prokaryotic life.\
*bioRxiv*. 

https://doi.org/10.64898/2025.12.30.695181

Lees JA, Tonkin-Hill G, Yang Z, Corander J.\
Mandrake: visualizing microbial population structure by embedding millions of genomes into a low-dimensional representation.\
*Philosophical Transactions of The Royal Society B*. 2022;377: 20210237.

https://doi.org/10.1098/rstb.2021.0237

We rely on algorithms from:

*bindash* (written by XiaoFei Zhao):\
Zhao, X. BinDash, software for fast genome distance estimation on a typical personal laptop.\
*Bioinformatics* **35**:671–673 (2019).\
doi:[10.1093/bioinformatics/bty651](https://dx.doi.org/10.1093/bioinformatics/bty651)

*ntHash* (written by Hamid Mohamadi):\
Mohamadi, H., Chu, J., Vandervalk, B. P. & Birol, I. ntHash: recursive nucleotide hashing.\
*Bioinformatics* **32**:3492–3494 (2016).\
doi:[10.1093/bioinformatics/btw397](https://dx.doi.org/10.1093/bioinformatics/btw397)