WarpSTR

WarpSTR determines tandem repeat lengths directly from raw nanopore sequencing signals to improve accuracy of short tandem repeat (STR) genotyping.

Key Features:

• Raw-signal analysis: Determines STR lengths directly from raw Oxford Nanopore signals without relying on basecalled sequences.
• Simple and complex repeat handling: Characterizes both simple and complex tandem repeats, including repeats with minor motif variations.
• Algorithmic approach: Employs a finite-state automaton combined with a search algorithm analogous to dynamic time warping to align signal patterns to repeat models.
• Improved accuracy: Demonstrated reduced mean absolute error in STR length estimates compared to basecalling-based methods and existing tools such as STRique in an evaluation of 241 STRs.
• Nanopore-read suitability: Designed for analysis of long reads produced by Oxford Nanopore sequencing, addressing basecalling unreliability in repetitive regions.

Scientific Applications:

• STR genotyping: Precise estimation of short tandem repeat lengths for research and clinical genotyping.
• Genomics research: Analysis of tandem-repeat variation in genomic studies that leverage long-read nanopore sequencing.
• Clinical diagnostics: Improved STR length determination for applications where repeat expansions or contractions have clinical relevance.

Methodology:

Analyzes raw nanopore signals using a finite-state automaton combined with a search algorithm analogous to dynamic time warping to locate and quantify tandem repeat motifs without using basecalled sequences.