S-conLSH

S-conLSH performs alignment-free gapped mapping of noisy long reads generated by Single Molecule, Real-Time (SMRT) sequencing using Spaced Context-based Locality Sensitive Hashing to locate reads on a reference genome.

Key Features:

• Alignment-Free Mapping: Uses multiple spaced patterns and Spaced Context-based Locality Sensitive Hashing to enable gapped mapping of reads without base-to-base alignment.
• Handling Genetic Variability: Detects distant homologies and maps reads across regions affected by genetic duplications and recombination.
• Performance Efficiency: Demonstrates at least a twofold speed improvement over state-of-the-art alignment-based methods while maintaining high accuracy.
• High Sensitivity: Achieves 99% sensitivity on human simulated sequence data for mapping noisy long reads.
• Flexible Output Formats: Produces results in PAF format by default and can optionally generate aligned output in SAM format.

Scientific Applications:

• Genome Assembly: Facilitates assembly tasks involving complex regions with duplications and recombination using SMRT long reads.
• Variant Detection: Supports identification of genetic variants in regions with high variability or repetitive sequences from noisy long-read data.
• Comparative Genomics: Enables analysis of distant homologies across species or within populations using long-read mappings.

Methodology:

S-conLSH applies Spaced Context-based Locality Sensitive Hashing by creating hash functions based on multiple spaced patterns that capture and compare subsequences of reads in a manner resilient to gaps and noise, enabling gapped mapping without traditional alignment.