This repository hosts a number of different projects related to minimizers.
- In src/lib.rs, reference implementations for the schemes presented in the mod-minimizer
paper with Giulio Ermanno Pibiri.
- See also this blogpost.
- These are also used for the lower bound paper with Bryce Kille:
- Python bindings available in src/py.rs.
- A fast implementation of random minimizers in src/par/, corresponding to this post.
- Computes the minimizers of a human genome in around two seconds.
- Code for the blogpost and corresponding benchmarks are in benches/blog and benches/bench.rs.
- Ongoing research on new sampling schemes.
- Plots and experiments are in py/plot.ipynb.
- Random minimizers.
- two versions of asymptotically optimal Rotational minimizers (Marçais et al., 2018) .
- Miniception, and a small slightly improved variant of it.
- Decycling and double decycling based minimizers (Pellow et al., 2023).
- Bidirectional anchors (Loukides et al., 2023)
- Mod-sampling, with lr-minimizers and mod-minimizers (our work).
