ArticleGigaScience2020
Sequence Compression Benchmark (SCB) database-A comprehensive evaluation of reference-free compressors for FASTA-formatted sequences.
Article in GigaScience, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- FFC: a scalable FASTA compressor.Bioinformatics (Oxford, England) · 2026Article
- MBGC2: Boosting compression via efficient encoding of approximate matches in genome collections.GigaScience · 2026Article
- Article
- A lossless reference-free sequence compression algorithm leveraging grammatical, statistical, and substitution rules.Briefings in functional genomics · 2025Article
- JARVIS3: an efficient encoder for genomic data.Bioinformatics (Oxford, England) · 2024Article
- Compression rates of microbial genomes are associated with genome size and base composition.Genomics & informatics · 2024Article
- A novel lossless encoding algorithm for data compression-genomics data as an exemplar.Frontiers in bioinformatics · 2024Article
- Bioinformatics tools for the sequence complexity estimates.Biophysical reviews · 2023Review
- The impact of altering emission data precision on compression efficiency and accuracy of simulations of the community multiscale air quality model.Geoscientific model development · 2023Article
- Enhancing genomic mutation data storage optimization based on the compression of asymmetry of sparsity.Frontiers in genetics · 2023Article
- Nanopore Sequencing Data Analysis of 16S rRNA Genes Using the GenomeSync-GSTK System.Methods in molecular biology (Clifton, N.J.) · 2023Article
- AlcoR: alignment-free simulation, mapping, and visualization of low-complexity regions in biological data.GigaScience · 2022Article
- Efficient compression of SARS-CoV-2 genome data using Nucleotide Archival Format.Patterns (New York, N.Y.) · 2022Review
- The complexity landscape of viral genomes.GigaScience · 2022Article
- Fast Phylogeny of SARS-CoV-2 by Compression.Entropy (Basel, Switzerland) · 2022Article
- MBGC: Multiple Bacteria Genome Compressor.GigaScience · 2022Article
- FUSTA: leveraging FUSE for manipulation of multiFASTA files at scale.Bioinformatics advances · 2022Article
- An Alignment-Independent Approach for the Study of Viral Sequence Diversity at Any Given Rank of Taxonomy Lineage.Biology · 2021Article
- AC2: An Efficient Protein Sequence Compression Tool Using Artificial Neural Networks and Cache-Hash Models.Entropy (Basel, Switzerland) · 2021Article
- Simplitigs as an efficient and scalable representation of de Bruijn graphs.Genome biology · 2021Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundNearly all molecular sequence databases currently use gzip for data compression. Ongoing rapid accumulation of stored data calls for a more efficient compression tool. Although numerous compressors exist, both specialized and general-purpose, choosing one of them was difficult because no comprehensive analysis of their comparative advantages for sequence compression was available.
findingsWe systematically benchmarked 430 settings of 48 compressors (including 29 specialized sequence compressors and 19 general-purpose compressors) on representative FASTA-formatted datasets of DNA, RNA, and protein sequences. Each compressor was evaluated on 17 performance measures, including compression strength, as well as time and memory required for compression and decompression. We used 27 test datasets including individual genomes of various sizes, DNA and RNA datasets, and standard protein datasets. We summarized the results as the Sequence Compression Benchmark database (SCB database, http://kirr.dyndns.org/sequence-compression-benchmark/), which allows custom visualizations to be built for selected subsets of benchmark results.
conclusionWe found that modern compressors offer a large improvement in compactness and speed compared to gzip. Our benchmark allows compressors and their settings to be compared using a variety of performance measures, offering the opportunity to select the optimal compressor on the basis of the data type and usage scenario specific to a particular application.
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