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HipSTR-UI: A cross-platform graphical interface for accessible str genotyping from next-generation sequencing data.
Tamara Soledad Frontanilla1, Matheus de Sousa Ferrari1, Jesus Ayala2
1Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP 14049-900, Brasil.
Forensic Science International. Genetics
|February 21, 2026
Summary
HipSTR-UI is a new graphical tool that simplifies next-generation sequencing analysis for forensic genetics. It automates Short Tandem Repeat genotyping, making advanced DNA analysis more accessible for human identification and kinship testing.
Area of Science:
- Forensic Genetics
- Bioinformatics
- Genomics
Background:
- Next-generation sequencing (NGS) offers high-resolution analysis of genetic markers like Short Tandem Repeats (STRs).
- Existing command-line tools for STR genotyping can present a steep learning curve for routine forensic applications.
Purpose of the Study:
- To develop HipSTR-UI, a user-friendly graphical interface for the HipSTR STR genotyping software.
- To automate and streamline the STR genotyping workflow from raw sequencing data to final genotype calls.
- To enhance the accessibility of advanced NGS-based forensic genetic analyses.
Main Methods:
- Developed a cross-platform graphical user interface (GUI) integrating precompiled HipSTR binaries.
- Automated the process of aligning sequencing reads (BAM/CRAM) to a reference genome (FASTA) and calling STR genotypes (VCF format).
- Validated HipSTR-UI using Phase 3 of the 1000 Genomes Project data.
Main Results:
- HipSTR-UI achieved 100% concordance with the established HipSTR command-line version in genotype calls.
- No discrepancies were observed in concordance rates, discordant loci, or quality scores between the GUI and command-line versions.
- The interface provides a graphical parameter panel and facilitates exportable results.
Conclusions:
- HipSTR-UI successfully combines the analytical power of HipSTR with an intuitive, multilingual interface.
- The tool bridges the gap between advanced sequencing technologies and routine forensic genetic workflows.
- HipSTR-UI is expected to facilitate the adoption of NGS-based STR analysis for human identification and kinship testing.
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