Abstract
MotivationCRAM 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.ResultsWith 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.Availability and implementationThe CRAM 3.0 specification is freely available from https://samtools.github.io/hts-specs/CRAMv3.pdf. The CRAM 3.1 improvements are available in a separate OpenSource HTScodecs library from https://github.com/samtools/htscodecs, and have been incorporated into HTSlib.Supplementary information Supplementary data are available at Bioinformatics online.
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