RENANO

RENANO compresses FASTQ files produced by nanopore sequencing using reference-based lossless algorithms to reduce storage size while preserving exact base call sequences.

Key Features:

• Reference-Based Compression: RENANO leverages a reference genome and implements two algorithms: Scenario 1 where the reference is available to both compressor and decompressor, and Scenario 2 where the reference is available only to the compressor with a compacted version included in the compressed file.
• Improved Compression Efficiency: Compared to ENANO, RENANO improves base call sequence compression by an average of 39.8% in Scenario 1 and by 15.2–49.0% in Scenario 2 depending on dataset coverage, improves total FASTQ compression by an average of 12.7%, and yields overall size reductions of 5.1–16.5% in Scenario 2.
• Lossless Compression: RENANO performs lossless compression, ensuring exact recovery of original FASTQ data upon decompression.
• Nanopore-Focused Enhancements: RENANO concentrates algorithmic improvements on base call sequence compression while maintaining other ENANO components to address large volumes and variable-length noisy reads produced by nanopore sequencers.

Scientific Applications:

• Nanopore sequencing data management: Reducing storage and transmission requirements for FASTQ datasets generated by nanopore sequencers.
• Genomic research workflows: Enabling more efficient handling of large-scale nanopore sequencing data to facilitate downstream analysis of sequencing results.

Methodology:

Using a reference genome to guide compression, implementing two algorithms for different reference-availability scenarios, and retaining other ENANO components while enhancing base call sequence compression.