biostudies-literature00440Bonfield JKWellcome Trust337-339https://www.ebi.ac.uk/biostudies/studies/S-EPMC6330002biostudies-literatureUnknown35(2)<h4>Motivation</h4>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.<h4>Results</h4>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).<h4>Availability and implementation</h4>Crumble is OpenSource and can be obtained from https://github.com/jkbonfield/crumble.<h4>Supplementary information</h4>Supplementary data are available at Bioinformatics online.Bioinformatics (Oxford, England)Crumble: reference free lossy compression of sequence quality values.PMC6330002207492/Z/17/ZWT098051McCarthy SABonfield JKDurbin R44falseCrumble: reference free lossy compression of sequence quality values.<h4>Motivation</h4>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.<h4>Results</h4>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).<h4>Availability and implementation</h4>Crumble is OpenSource and can be obtained from https://github.com/jkbonfield/crumble.<h4>Supplementary information</h4>Supplementary data are available at Bioinformatics online.2019-01-01T00:00:00Z2019 Jan2021-02-20T23:37:48Z2019-03-26T22:37:10ZS-EPMC63300022999228810.1093/bioinformatics/bty608