Fast and flexible minimizer digestion with digest.
Where this comes from
- Record sourced from PubMed, PMID 40581603.
- Also identified by DOI 10.1093/bioinformatics/btaf368 and PMC identifier 12233085.
- Licence recorded as CC BY.
- The licence permits redistribution, so the abstract is shown in full and the full text is available from the publisher.
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.
Medical subject headings
- Software
- Genomics
- Computational Biology
- Sequence Analysis, DNA