ArticleBioinformatics (Oxford, England)2015
QVZ: lossy compression of quality values.
Article in Bioinformatics (Oxford, England), 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- PQSDC: a parallel lossless compressor for quality scores data via sequences partition and run-length prediction mapping.Bioinformatics (Oxford, England) · 2024Article
- 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
- 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
- FCLQC: fast and concurrent lossless quality scores compressor.BMC bioinformatics · 2021Article
- LCQS: an efficient lossless compression tool of quality scores with random access functionality.BMC bioinformatics · 2020Article
- Better quality score compression through sequence-based quality smoothing.BMC bioinformatics · 2019Article
- Denoising of Aligned Genomic Data.Scientific reports · 2019Article
- SPRING: a next-generation compressor for FASTQ data.Bioinformatics (Oxford, England) · 2019Article
- MassComp, a lossless compressor for mass spectrometry data.BMC bioinformatics · 2019Article
- Crumble: reference free lossy compression of sequence quality values.Bioinformatics (Oxford, England) · 2019Article
- CALQ: compression of quality values of aligned sequencing data.Bioinformatics (Oxford, England) · 2018Article
- Compression of genomic sequencing reads via hash-based reordering: algorithm and analysis.Bioinformatics (Oxford, England) · 2018Article
- GeneComp, a new reference-based compressor for SAM files.Proceedings. Data Compression Conference · 2017Article
- 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
- Towards precision medicine.Nature reviews. Genetics · 2016Review
- CARGO: effective format-free compressed storage of genomic information.Nucleic acids research · 2016Article
- An Evaluation Framework for Lossy Compression of Genome Sequencing Quality Values.Proceedings. Data Compression ConferenceArticle
Corrections and comments
- Erratum issued
Authors and funding
6 authors.
Funding
Abstract
motivationRecent advancements in sequencing technology have led to a drastic reduction in the cost of sequencing a genome. This has generated an unprecedented amount of genomic data that must be stored, processed and transmitted. To facilitate this effort, we propose a new lossy compressor for the quality values presented in genomic data files (e.g. FASTQ and SAM files), which comprise roughly half of the storage space (in the uncompressed domain). Lossy compression allows for compression of data beyond its lossless limit.
resultsThe proposed algorithm QVZ exhibits better rate-distortion performance than the previously proposed algorithms, for several distortion metrics and for the lossless case. Moreover, it allows the user to define any quasi-convex distortion function to be minimized, a feature not supported by the previous algorithms. Finally, we show that QVZ-compressed data exhibit better performance in the genotyping than data compressed with previously proposed algorithms, in the sense that for a similar rate, a genotyping closer to that achieved with the original quality values is obtained. AVAILABILITY AND IMPLEMENTATION: QVZ is written in C and can be downloaded from https://github.com/mikelhernaez/qvz. CONTACT: mhernaez@stanford.edu or gmalysa@stanford.edu or iochoa@stanford.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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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.