lordFAST: sensitive and Fast Alignment Search Tool for LOng noisy Read sequencing Data.

Area of Science:

• Genomics
• Bioinformatics
• Computational Biology

Background:

• High-throughput sequencing (HTS) advances genomics and precision medicine by analyzing human genomes.
• Short read lengths from HTS technologies limit accurate analysis of genomic repeats.
• Single molecule sequencing (SMS) offers longer reads but suffers from high error rates, complicating downstream analysis.

Purpose of the Study:

• To develop a novel long-read mapper designed for single molecule sequencing (SMS) technologies.
• To improve the accuracy and efficiency of aligning long reads to reference genomes.
• To address the challenges posed by high error rates in SMS data for variant detection.

Main Methods:

• Introduction of lordFAST, a C++ implemented, multi-threaded long-read mapper.
• Designed specifically for aligning reads from PacBio and similar SMS technologies.
• Optimized for high sensitivity, speed, and low memory footprint.

Main Results:

• lordFAST demonstrates higher sensitivity compared to existing long-read mappers.
• It is among the fastest available mappers for SMS data.
• The tool exhibits a low memory footprint, enhancing its practicality.

Conclusions:

• lordFAST effectively addresses the challenges of mapping long, error-prone reads from SMS technologies.
• The tool enhances the utility of SMS data for genomic variation studies.
• lordFAST provides a sensitive, fast, and memory-efficient solution for long-read alignment.