FFC: a scalable FASTA compressor.
basic_science · Level V
Where this comes from
- Record sourced from PubMed, PMID 41872022.
- Also identified by DOI 10.1093/bioinformatics/btag132 and PMC identifier 13038249.
- Licence recorded as CC BY.
- The licence permits redistribution, so the abstract is shown in full and the full text is available from the publisher.
Abstract
FASTA is a widely used text-based format for storing nucleotide and protein sequences. The existing FASTA compressors usually focus on (slightly) improving the compression ratio, not on practical performance. We present FFC, a scalable FASTA compressor that achieves average compression speeds 4.7× and 11.4× higher than two high-performance compressors, zstd and NAF, respectively, across a benchmark set of seven single genomes. It also delivers average decompression speeds 3.5× and 2.7× higher than zstd and NAF, respectively. Although a chunk-based zstd variant with parallel decompression, pzstd, almost matches FFC speed, its compression ratio is on average by 23% worse than FFC's. For the experiment, a 14-core workstation and a RAM disk (to reduce the impact of I/O) were used. FFC is freely available at github.com/kowallus/ffc and also as a Zenodo repository at 10.5281/zenodo.18892353, and the used datasets at 10.5281/zenodo.18873744.
Medical subject headings
- Software
- Data Compression
- Computational Biology