ArticleBMC bioinformatics2013
QualComp: a new lossy compressor for quality scores based on rate distortion theory.
Article in BMC bioinformatics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- zDUR: reference-free FASTQ compressor with high compression ratio and speed.BMC bioinformatics · 2026Article
- PQSDC: a parallel lossless compressor for quality scores data via sequences partition and run-length prediction mapping.Bioinformatics (Oxford, England) · 2024Article
- A Pipeline for Constructing Reference Genomes for Large Cohort-Specific Metagenome Compression.Microorganisms · 2023Article
- Nanopore quality score resolution can be reduced with little effect on downstream analysis.Bioinformatics advances · 2022Article
- IonCRAM: a reference-based compression tool for ion torrent sequence files.BMC bioinformatics · 2020Article
- Better quality score compression through sequence-based quality smoothing.BMC bioinformatics · 2019Article
- Effect of lossy compression of quality scores on variant calling.Briefings in bioinformatics · 2017Article
- CROMqs: an infinitesimal successive refinement lossy compressor for the quality scores.Proceedings. Information Theory Workshop · 2016Article
- Computational Biology in the 21st Century: Scaling with Compressive Algorithms.Communications of the ACM · 2016Article
- Novel bioinformatic developments for exome sequencing.Human genetics · 2016Review
- MetaCRAM: an integrated pipeline for metagenomic taxonomy identification and compression.BMC bioinformatics · 2016Article
- QVZ: lossy compression of quality values.Bioinformatics (Oxford, England) · 2015Article
- Data-dependent bucketing improves reference-free compression of sequencing reads.Bioinformatics (Oxford, England) · 2015Article
- Reference-based compression of short-read sequences using path encoding.Bioinformatics (Oxford, England) · 2015Article
- Light-weight reference-based compression of FASTQ data.BMC bioinformatics · 2015Article
- Quality score compression improves genotyping accuracy.Nature biotechnology · 2015Article
- Sequence Factorization with Multiple References.PloS one · 2015Article
- Aligned genomic data compression via improved modeling.Journal of bioinformatics and computational biology · 2014Article
- Traversing theResearch in computational molecular biology : ... Annual International Conference, RECOMB ... : proceedings. RECOMB (Conference : 2005- ) · 2014Article
- Data compression for sequencing data.Algorithms for molecular biology : AMB · 2013Article
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundNext Generation Sequencing technologies have revolutionized many fields in biology by reducing the time and cost required for sequencing. As a result, large amounts of sequencing data are being generated. A typical sequencing data file may occupy tens or even hundreds of gigabytes of disk space, prohibitively large for many users. This data consists of both the nucleotide sequences and per-base quality scores that indicate the level of confidence in the readout of these sequences. Quality scores account for about half of the required disk space in the commonly used FASTQ format (before compression), and therefore the compression of the quality scores can significantly reduce storage requirements and speed up analysis and transmission of sequencing data.
resultsIn this paper, we present a new scheme for the lossy compression of the quality scores, to address the problem of storage. Our framework allows the user to specify the rate (bits per quality score) prior to compression, independent of the data to be compressed. Our algorithm can work at any rate, unlike other lossy compression algorithms. We envisage our algorithm as being part of a more general compression scheme that works with the entire FASTQ file. Numerical experiments show that we can achieve a better mean squared error (MSE) for small rates (bits per quality score) than other lossy compression schemes. For the organism PhiX, whose assembled genome is known and assumed to be correct, we show that it is possible to achieve a significant reduction in size with little compromise in performance on downstream applications (e.g., alignment).
conclusionsQualComp is an open source software package, written in C and freely available for download at https://sourceforge.net/projects/qualcomp.
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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.