Tidk: a Toolkit to Rapidly Identify Telomeric Repeats from Genomic Datasets

Overview

Journal Bioinformatics

Publisher Oxford University Press

Date 2025 Feb 1

PMID 39891350

Authors

Max R Brown

Pablo Manuel Gonzalez de La Rosa

Pablo Gonzalez de La Rosa

Mark Blaxter

Affiliations

Soon will be listed here.

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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