YALFF

YALFF compresses FASTQ files by smoothing per-base quality scores to reduce entropy and improve compressibility while preserving information required for SNP calling and genotyping from next-generation sequencing (NGS) data.

Key Features:

• Quality Score Smoothing: Applies a smoothing algorithm that adjusts per-read quality scores to reduce entropy and improve compressibility while preserving information for downstream analyses such as SNP calling.
• FM-Index Utilization: Leverages the FM-Index (a compressed suffix array) to represent and manage k-mers, enabling a succinct k-mer dictionary that can be linearized into contigs and reducing memory requirements compared to tools like QUARTZ or GeneCodeq.
• Resource Efficiency: Operates with a low memory footprint, requiring approximately 5.7 GB of free RAM.
• Improved Genotyping Accuracy: Performs quality-score smoothing in a manner that maintains or can improve the precision of genotyping pipelines.

Scientific Applications:

• Large-scale NGS data storage: Reduces FASTQ file size for projects that generate large volumes of sequencing data to lessen storage burden.
• SNP calling and genotyping pipelines: Preserves the information needed for accurate SNP calling and genotyping after compression.

Methodology:

YALFF uses an FM-Index-based compressed representation of k-mers (forming a succinct dictionary linearized into contigs) and a quality score smoothing algorithm that adjusts quality values to reduce entropy and improve compressibility.