STRprofiler

STRprofiler is a software tool designed to profile short tandem repeats (STRs) in DNA sequence data. It is used in forensic genetics, clinical genetics, and population genetics to determine STR allele sizes and genotypes across a predefined panel of loci. STRprofiler accepts sequencing reads from next-generation platforms or fragment-size data from PCR-based assays, and outputs a locus-by-locus genotype table along with quality metrics.

Key features include locus-level analysis across multiple STR loci, platform-agnostic input handling, automatic normalization to reference coordinates, allele calling with probabilistic models, and optional stutter correction. The tool provides detailed reports, supports standard STR panels, and exports results in common formats (CSV/TSV, VCF-like tables) suitable for downstream analysis.

Algorithm and workflow: STRprofiler aligns or assembles reads around each STR locus, estimates the repeat count using repeat-aware modeling of read lengths and fragment sizes, and integrates per-read evidence into a genotype call with confidence scores. It models sequencing or PCR-induced artifacts such as stutter and dropout and applies locus-specific filters to reduce false positives.

Applications and limitations: It supports forensic identity testing, paternity and kinship analyses, and population studies. Validation requirements apply, and performance depends on data quality and the complexity of the locus. In loci with long repeats or interruptions, calls may be ambiguous and require manual review.

Availability and interoperability: STRprofiler is compatible with standard data formats (FASTQ, BAM, VCF-like outputs) and can be integrated into common analysis pipelines. Documentation and tutorials describe installation, parameter tuning, and interpretation of results.