short-tandem-repeats

Small variant, structural variant, and short tandem repeat phasing tool for PacBio HiFi reads

Detect novel (and reference) STR expansions from short-read data

Tool to annotate outfiles from ExpansionHunter and TRGT with the pathologic implications of the repeat

tandemtwister: Tandem repeat genotyping tool

NanoRepeat: fast and accurate analysis of Short Tandem Repeats (STRs) from Oxford Nanopore sequencing data

STRspy: a novel alignment and quantification-based state-of-the-art method, short tandem repeat (STR) detection calling tool designed specifically for long-read sequencing reads such as from Oxford nanopore technology (ONT) and PacBio.

A python package, command-line tool, and Shiny application to compare short tandem repeat (STR) profiles.

Computational, High-throughput Individual Identification through Microsatellite Profiling

Microsatellite genotyping

Detect short tandem repeats (STRs) and call repeat expansions from long-read (Oxford Nanopore) BAM files — motif discovery, per-allele repeat length, coverage, and visual reports.

Supporting code for the microsatellite genotyping paper introducing CHIIMP

🧬 A curated list of awesome resources for repeat DNA research

Allele-specific expression (ASE) for short tandem repeats (STRs)

STRhub: an open-source forensic STR data explorer Web platform for visualization, comparison and education about Short Tandem Repeats (STRs) across populations. Built with Next.js, shadcn/ui, and genomic datasets (1000 Genomes, HGDP, NIST STRBase).

Forensic and statistical genetics

Detection and classfication of short tandem repeats in read data

🧬 recombination and mutation rates inference from polymorphisms (STRs, SNPs and INDELs) along the X chromosome

Nextflow pipeline for ultrasensitive STR analysis

Converts a STRidER frequency table XML to FrequencyDb

Adds Stranger's pathogenicity thresholds to an ExpansionHunter catalog, matched from STRchive by position.