Crumble: reference free lossy compression of sequence quality values.

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.

SUBMITTER: Bonfield JK 

PROVIDER: S-EPMC6330002 | biostudies-literature | 2019 Jan

REPOSITORIES: biostudies-literature