STRaitRazor

STRaitRazor analyzes massively parallel sequencing (MPS) data to detect and characterize short tandem repeats, single nucleotide polymorphisms, insertion/deletions, and mitochondrial DNA haplotypes for allele and haplotype interpretation.

Key Features:

• Supported marker systems: Handles short tandem repeats (STRs), single nucleotide polymorphisms (SNPs), insertion/deletions (indels), and mitochondrial DNA (mtDNA).
• Input and batch processing: Processes fastq files and primary analysis outputs in batch for large-scale datasets.
• Haplotype pileup analysis: Performs secondary analysis of STRaitRazor haplotype pileups.
• Sequence-based allele conversion: Converts sequence-based allele calls into genotype tables and bar plots for downstream analysis.
• Threshold-based genotype calling: Applies user-controllable thresholds such as heterozygous balance and strand balance for genotype calls.
• Report generation: Produces individual report folders and locus- and haplotype-level summary reports.
• Preliminary triage system: Identifies potential alleles and flags loci with suspected severe heterozygote imbalance.

Scientific Applications:

• Forensic genetics: Enables sequence-based STR and SNP allele and haplotype interpretation from MPS data for forensic analyses.
• Population studies: Facilitates population genetics analyses using sequence-based alleles and haplotypes from STRs, SNPs, indels, and mtDNA.
• Reference sample triage: Supports preliminary triaging of single-source, reference samples by identifying potential alleles and imbalance.
• Validation/concordance: Demonstrates concordance with manually curated datasets, with a reported 98.72% consistency rate.

Methodology:

Batch processing of fastq files and primary analysis outputs; secondary analysis of STRaitRazor haplotype pileups; conversion of sequence-based allele calls into genotype tables and bar plots; application of heterozygous balance and strand balance thresholds for genotype calls; generation of individual report folders and locus- and haplotype-level summary reports; preliminary triaging to identify potential alleles and flag loci with severe heterozygote imbalance.