TideHunter

TideHunter detects tandem repeat patterns and calls consensus sequences from noisy long-read sequencing data (Pacific Biosciences and Oxford Nanopore Technologies) to improve accuracy of tandem repeat characterization.

Key Features:

• Efficiency and Sensitivity: Handles noisy long reads with error rates up to 20%, providing high sensitivity and accuracy while reporting performance tens of times faster than prior methods.
• No Limit on Repeat Pattern Size: Imposes no restrictions on the maximal size of repeat patterns, enabling analysis of large and complex tandem repeats.
• Integration with Rolling Circle Amplification (RCA): Optimized to process linear products generated from RCA by collapsing tandem sequences into consensus sequences to improve accuracy over raw reads.
• Sequencing Technology Compatibility: Supports Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT) long-read sequencing data.
• Implementation: Implemented in C for performance efficiency.
• Benchmarking: Performance has been evaluated on simulated and real datasets with varying error rates and repeat pattern sizes.

Scientific Applications:

• Genomic Research: Facilitates study of complex genomic regions that are rich in repetitive sequences.
• Structural Variant Analysis: Enhances detection and characterization of structural variants within genomes by resolving tandem repeats.
• Disease Genomics: Improves accuracy of sequencing data used to identify genetic mutations associated with disease through consensus calling of tandem repeats.

Methodology:

Employs a novel seed-and-chain approach to discover tandem repeat patterns from amplified long-read sequencing data, collapses detected tandem repeats into consensus sequences, and benchmarks performance on simulated and real datasets with varying error rates and repeat pattern sizes.