ArticlePloS one2013
Compression of FASTQ and SAM format sequencing data.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 66 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
66 citing papers in PubMed.
- zDUR: reference-free FASTQ compressor with high compression ratio and speed.BMC bioinformatics · 2026Article
- MBGC2: Boosting compression via efficient encoding of approximate matches in genome collections.GigaScience · 2026Article
- FastqCA: an effective FASTQ compressor through 2D spatial redundancy reduction.Frontiers in genetics · 2026Article
- Investigation of the Impact of miRNA-7151 and a Mutation in Its Target Gene lncRNABiomedicines · 2025Article
- PgRC2: engineering the compression of sequencing reads.Bioinformatics (Oxford, England) · 2025Article
- A lossless reference-free sequence compression algorithm leveraging grammatical, statistical, and substitution rules.Briefings in functional genomics · 2025Article
- OReO: optimizing read order for practical compression.Bioinformatics advances · 2025Article
- JARVIS3: an efficient encoder for genomic data.Bioinformatics (Oxford, England) · 2024Article
- PQSDC: a parallel lossless compressor for quality scores data via sequences partition and run-length prediction mapping.Bioinformatics (Oxford, England) · 2024Article
- A novel lossless encoding algorithm for data compression-genomics data as an exemplar.Frontiers in bioinformatics · 2024Article
- A Pipeline for Constructing Reference Genomes for Large Cohort-Specific Metagenome Compression.Microorganisms · 2023Article
- Ten quick tips for bioinformatics analyses using an Apache Spark distributed computing environment.PLoS computational biology · 2023Article
- Navigating bottlenecks and trade-offs in genomic data analysis.Nature reviews. Genetics · 2023Review
- Efficient sequencing data compression and FPGA acceleration based on a two-step framework.Frontiers in genetics · 2023Article
- Efficient compression of SARS-CoV-2 genome data using Nucleotide Archival Format.Patterns (New York, N.Y.) · 2022Review
- CMIC: an efficient quality score compressor with random access functionality.BMC bioinformatics · 2022Article
- ACO:lossless quality score compression based on adaptive coding order.BMC bioinformatics · 2022Article
- CoLoRd: compressing long reads.Nature methods · 2022Article
- The Sequence Read Archive: a decade more of explosive growth.Nucleic acids research · 2022Article
- FCLQC: fast and concurrent lossless quality scores compressor.BMC bioinformatics · 2021Article
6 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
Abstract
Storage and transmission of the data produced by modern DNA sequencing instruments has become a major concern, which prompted the Pistoia Alliance to pose the SequenceSqueeze contest for compression of FASTQ files. We present several compression entries from the competition, Fastqz and Samcomp/Fqzcomp, including the winning entry. These are compared against existing algorithms for both reference based compression (CRAM, Goby) and non-reference based compression (DSRC, BAM) and other recently published competition entries (Quip, SCALCE). The tools are shown to be the new Pareto frontier for FASTQ compression, offering state of the art ratios at affordable CPU costs. All programs are freely available on SourceForge. Fastqz: https://sourceforge.net/projects/fastqz/, fqzcomp: https://sourceforge.net/projects/fqzcomp/, and samcomp: https://sourceforge.net/projects/samcomp/.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.