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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