RabbitFX

High-performance FASTA and FASTQ parsing framework

RabbitFX accelerates parsing of FASTA and FASTQ files by implementing optimized, lightweight file-reading and formatting strategies that exploit multi-core CPUs and high-speed storage to improve throughput for large next-generation sequencing (NGS) datasets.

Key Features:

• Optimized FASTA/FASTQ Parsing: Implements lightweight parsing and advanced formatting to reduce I/O bottlenecks and execution time for large-scale sequencing data.
• Modular C++ APIs: Provides modular C++ application programming interfaces for integration into bioinformatics pipelines and I/O-intensive tools.
• Demonstrated Performance Gains: Achieves ≥11.6× speedup (6.6× on gzip-compressed files) in fastp, 2.4× (2.4× on compressed files) in Ktrim, and 3.7× (3.2× on compressed files) in Mash compared to original implementations.

Scientific Applications:

• Next-Generation Sequencing Data Processing: Enhances performance of I/O-intensive NGS tools, including fastp, Ktrim, and Mash, for large FASTA and FASTQ datasets.

Methodology:

RabbitFX employs a lightweight FASTA/FASTQ parsing architecture combined with optimized data formatting to maximize parallel CPU utilization and storage throughput, minimizing file parsing bottlenecks in high-volume sequencing workflows.