ArticleBioinformatics (Oxford, England)2019
Crumble: reference free lossy compression of sequence quality values.
Article in Bioinformatics (Oxford, England), 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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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.
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Who cites it
10 citing papers in PubMed.
- An Icelandic pangenome reference.Nature · 2026Article
- PQSDC: a parallel lossless compressor for quality scores data via sequences partition and run-length prediction mapping.Bioinformatics (Oxford, England) · 2024Article
- Extensive Phylogenomic Discordance and the Complex Evolutionary History of the Neotropical Cat Genus Leopardus.Molecular biology and evolution · 2023Article
- Cloud-native distributed genomic pileup operations.Bioinformatics (Oxford, England) · 2023Article
- Approach to Cohort-Wide Re-Analysis of Exome Data in 1000 Individuals with Neurodevelopmental Disorders.Genes · 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
- Twelve years of SAMtools and BCFtools.GigaScience · 2021Article
- Performance evaluation of lossy quality compression algorithms for RNA-seq data.BMC bioinformatics · 2020Article
- Cram-JS: reference-based decompression in node and the browser.Bioinformatics (Oxford, England) · 2019Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Motivation: The bulk of space taken up by NGS sequencing CRAM files consists of per-base quality values. Most of these are unnecessary for variant calling, offering an opportunity for space saving. Results: On the Syndip test set, a 17 fold reduction in the quality storage portion of a CRAM file can be achieved while maintaining variant calling accuracy. The size reduction of an entire CRAM file varied from 2.2 to 7.4 fold, depending on the non-quality content of the original file (see Supplementary Material S6 for details). Availability and implementation: Crumble is OpenSource and can be obtained from https://github.com/jkbonfield/crumble. 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.