Fast alignment-free similarity estimation methods in Rust.

Overview

This repository contains command-line executables that estimate the edit distance between query and reference sequences using:

1. Jaccard similarity of k-mer bags.
2. Jaccard similarity of strobemer bags.

Progress

• Minstrobes implemented and tested.
• 10,000-nt sequences with pre-computed edit distance generated for comparison with seed-bag-comparison estimates ((/data/experiment3)[/data/experiment3_100_query_higher_res]).

Development

• Randstrobes and Hybridstrobes