Fast and flexible minimizer digestion with digest

TL;DR

The paper introduces a new open-source tool called 'digest' for efficiently processing genomic sequences using minimizers, modimizers, or syncmers.

Contribution

The novel contribution is a fast and flexible implementation of minimizer digestion with efficient data structures and multi-threading support.

Findings

Digest can efficiently produce digests based on minimizers, modimizers, or syncmers.

The tool scales well to many threads and produces digests with expected spacings between elements.

Digest is implemented in C++17 with Python and Rust bindings for accessibility.

Abstract

Minimizer digestion is an increasingly common component of bioinformatics tools, including tools for de Bruijn graph assembly and sequence classification. We describe a new open source tool and library to facilitate efficient digestion of genomic sequences. It can produce digests based on the related ideas of minimizers, modimizers or syncmers. Digest uses efficient data structures, scales well to many threads, and produces digests with expected spacings between digested elements.

Digest is implemented in C++17 with a Python API, and is available open-source at https://github.com/VeryAmazed/digest. The python library is available on Bioconda. Rust bindings are available as a public crate at https://crates.io/crates/digest-rs.

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