Crumble: reference free lossy compression of sequence quality values
Open Access
- 10 July 2018
- journal article
- research article
- Published by Oxford University Press (OUP) in Bioinformatics
- Vol. 35 (2) , 337-339
Abstract
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. 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). Crumble is OpenSource and can be obtained from https://github.com/jkbonfield/crumble. Supplementary data are available at Bioinformatics online.Keywords
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Funding Information
- Wellcome Trust (WT098051)
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