NanoSpring

NanoSpring compresses nanopore sequencing reads in FASTQ format (including uncompressed and gzipped inputs) using a reference-free, assembly-based approach to reduce storage of base sequences.

Key Features:

• Reference-free compression: Implements a reference-free approach based on approximate assembly techniques for compressing read sequences.
• Nanopore-specific design: Tailored to the characteristics of nanopore sequencing data, including long reads and real-time processing considerations.
• FASTQ base-sequence focus: Operates on base sequences within FASTQ files for compression.
• Input formats: Supports both uncompressed and gzipped FASTQ inputs.
• Compression performance: Achieves compression rates of 0.35 to 0.65 bits per base.
• Comparison to general compressors: Provides 3 to 6 times better compression than general-purpose compressors such as gzip.
• Decompression speed: Outperforms the state-of-the-art tool CoLoRd in decompression speed while maintaining competitive compression ratios and resource usage.
• Dataset validation: Tested on diverse datasets including bacterial, metagenomic, plant, animal, and human whole-genome sequences.

Scientific Applications:

• Nanopore data storage and archival: Reduces storage footprint of nanopore FASTQ datasets for long-term archival.
• Real-time nanopore workflows: Supports workflows that require rapid data retrieval during nanopore sequencing runs.
• Metagenomic sequencing compression: Applicable to compression of metagenomic read datasets.
• Whole-genome sequencing data management: Applicable to bacterial, plant, animal, and human whole-genome sequencing read datasets.

Methodology:

NanoSpring uses a reference-free approach based on approximate assembly techniques applied to base sequences in FASTQ files, specifically tailored for long nanopore reads and real-time processing characteristics.