STRspy

STRspy performs short tandem repeat (STR) detection and sequence-level allele designation in long-read sequencing data from Oxford Nanopore Technologies (ONT) and PacBio platforms for forensic and genetic analyses.

Key Features:

• Long-Read Sequencing Compatibility: Optimized for long-read sequencing technologies including Oxford Nanopore Technologies (ONT) and PacBio.
• Length- and Sequence-Based Allele Designation: Integrates read sequence information with fragment length to assign alleles at STR loci.
• Forensic Applicability: Produces STR profiles and flanking variation suitable for forensic human identification workflows.
• Robust Genotyping Performance: In a proof-of-principle study using the ONT MinION with 30 PCR cycles, achieved 100% concordance with validated autosomal STR genotypes.
• Flanking Region SNP Identification: Detects single nucleotide polymorphisms in STR flanking regions with over 90% accuracy.
• Custom Database Integration: Processes basecalled reads against a custom allele database derived from STRSeq BioProject NIST 1036 for allele designation.
• Multiplex Panel Profiling: Profiles entire panels of autosomal STRs amplified by commercially available multiplex systems.

Scientific Applications:

• Forensic STR profiling: Generates length- and sequence-level STR profiles plus flanking SNPs to enhance discrimination in human identification.
• Nanopore feasibility in forensics: Demonstrates the feasibility of using ONT (e.g., MinION) long-read sequencing for STR panels despite prior concerns about error rates.
• Autosomal STR panel analysis: Enables profiling of complete autosomal STR panels amplified by commercial multiplex kits.

Methodology:

Processes basecalled long-read sequencing reads against a custom allele database (STRSeq BioProject NIST 1036) to perform length- and sequence-based allele designation and to identify SNPs in STR flanking regions.