SCB

SCB benchmarks reference-free compressors for FASTA-formatted nucleotide and peptide sequences to evaluate compression performance across multiple metrics.

Key Features:

• Reference-free FASTA benchmarking: Benchmarks reference-free compressors for FASTA-formatted nucleotide and peptide sequences.
• Compressor set: Evaluates 48 compressors, encompassing specialized sequence compressors and general-purpose compressors.
• Settings explored: Tests 430 distinct compressor settings across the evaluated compressors.
• Performance metrics: Measures 17 metrics, including compression strength (compression ratio), compression time, decompression time, and memory usage during compression and decompression.
• Test datasets: Uses 27 test datasets representing individual genomes of varying sizes, DNA and RNA sequences, and standard protein datasets.
• SCB database: Stores detailed benchmark results in the Sequence Compression Benchmark (SCB) database.
• Custom visualizations: Provides custom visualization support for analyzing selected subsets of compressors, settings, and datasets.
• Comparative findings: Reports comparative analyses demonstrating modern compressors outperform gzip in compactness and speed.

Scientific Applications:

• Compressor evaluation and comparison: Enables systematic comparison of reference-free sequence compressors on FASTA data using multiple performance metrics.
• Compressor and setting selection for sequence types: Supports selection of compressors and settings optimized for DNA, RNA, or protein datasets.
• Storage and processing optimization: Informs choices to improve storage efficiency and reduce processing time for large sequence databases.

Methodology:

Benchmarks 48 compressors across 430 settings on 27 FASTA test datasets and records 17 performance metrics for compression and decompression, with results stored in the SCB database and available for custom visualization.