{"database":"biostudies-literature","file_versions":[],"scores":{"citationCount":0,"reanalysisCount":0,"viewCount":44,"searchCount":0},"additional":{"submitter":["Bonfield JK"],"funding":["Wellcome Trust"],"pagination":["337-339"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC6330002"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["35(2)"],"pubmed_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."],"journal":["Bioinformatics (Oxford, England)"],"pubmed_title":["Crumble: reference free lossy compression of sequence quality values."],"pmcid":["PMC6330002"],"funding_grant_id":["207492/Z/17/Z","WT098051"],"pubmed_authors":["McCarthy SA","Bonfield JK","Durbin R"],"view_count":["44"],"additional_accession":[]},"is_claimable":false,"name":"Crumble: reference free lossy compression of sequence quality values.","description":"

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.","dates":{"release":"2019-01-01T00:00:00Z","publication":"2019 Jan","modification":"2021-02-20T23:37:48Z","creation":"2019-03-26T22:37:10Z"},"accession":"S-EPMC6330002","cross_references":{"pubmed":["29992288"],"doi":["10.1093/bioinformatics/bty608"]}}