CRAM 3.1: Advances in the CRAM file format

Abstract

Motivation: CRAM has established itself as a high compression alternative to the BAM file format for DNA sequencing data. We describe updates to further improve this on modern sequencing instruments. Results: With Illumina data CRAM 3.1 is 7-15% smaller than the equivalent CRAM 3.0 file, and 50-70% smaller than the corresponding BAM file. Long-read technology shows more modest compression due to the presence of high-entropy signals.