lordFAST

lordFAST aligns noisy long reads from single-molecule sequencing technologies (Pacific Biosciences and Oxford Nanopore) to reference genomes to enable accurate mapping and downstream genome analyses.

Key Features:

• Long-read alignment: Aligns long reads generated by single-molecule sequencing technologies, specifically Pacific Biosciences and Oxford Nanopore, to reference genomes.
• Error tolerance: Handles high SMS sequencing error rates to help distinguish sequencing errors from genuine genomic variants.
• High-throughput optimization: Designed for processing large SMS datasets to support increased instrument throughput.
• Speed and sensitivity: Reports improved speed and sensitivity compared to existing long-read mappers.
• Implementation: Implemented in C++ using efficient computational strategies to minimize memory footprint.
• Multi-threading: Supports multi-threading to utilize multiple CPU cores for faster alignment.

Scientific Applications:

• Genomics: Improves mapping in repetitive regions by leveraging long-read information to resolve genomic repeats.
• Variant detection: Supports downstream analyses that distinguish true genomic variants from sequencing errors in SMS data.
• Precision medicine: Enhances long-read mapping accuracy relevant to studies in genomics and precision medicine.

Methodology:

Implemented in C++ with efficient computational strategies, multi-threading, and a minimal memory footprint for optimized long-read mapping of high-throughput SMS datasets.