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Fast and flexible minimizer digestion with digest

Authors: Alan Zheng; Ishmeal Lee; Vikram S. Shivakumar; Omar Y. Ahmed; Ben Langmead;

Fast and flexible minimizer digestion with digest

Abstract

Abstract Summary 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. Availability and implementation 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.

Keywords

Applications Note, Computational Biology, Genomics, Sequence Analysis, DNA, Article, Software, Algorithms

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selected citations
These citations are derived from selected sources.
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
1
Average
Average
Average
Green
gold