tidk: a toolkit to rapidly identify telomeric repeats from genomic datasets.

Max R Brown; Pablo Manuel Gonzalez de La Rosa; Mark Blaxter

doi:10.1093/bioinformatics/btaf049

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tidk: a toolkit to rapidly identify telomeric repeats from genomic datasets.

Max R Brown·Pablo Manuel Gonzalez de La Rosa·Mark Blaxter

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Abstract

SUMMARY: "tidk" (short for telomere identification toolkit) uses a simple, fast algorithm to scan long DNA reads for the presence of short tandemly repeated DNA in runs, and to aggregate them based on canonical DNA string representation. These are telomeric repeat candidates. Our algorithm is shown to be accurate in genomes for which the telomeric repeat unit is known and is tested across a wide variety of newly assembled genomes to uncover new telomeric repeat units. Tools are provided to identify telomeric repeats de novo, scan genomes for known telomeric repeats, and to visualize telomeric repeats on the assembly. "tidk" is implemented in Rust and is available as a command line tool which can be compiled using the Rust toolchain or downloaded as a binary from bioconda. AVAILABILITY AND IMPLEMENTATION: The "tidk" Rust crate is freely available under the MIT license (https://crates.io/crates/tidk), and the source code is available at https://github.com/tolkit/telomeric-identifier.

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Telomere Software Algorithms Genomics Sequence Analysis, DNA Humans Repetitive Sequences, Nucleic Acid Journal Article Research Support, Non-U.S. Gov't

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Max R Brown, Pablo Manuel Gonzalez de La Rosa, Mark Blaxter. 2025-02-04. tidk: a toolkit to rapidly identify telomeric repeats from genomic datasets.. https://doi.org/10.1093/bioinformatics%2Fbtaf049

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