CRAM 3.1: advances in the CRAM file format.
Where this comes from
- Record sourced from PubMed, PMID 34999766.
- Also identified by DOI 10.1093/bioinformatics/btac010 and PMC identifier 8896640.
- Licence recorded as CC BY.
- The licence permits redistribution, so the abstract is shown in full and the full text is available from the publisher.
Abstract
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. 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. The 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 data are available at Bioinformatics online.
Medical subject headings
- High-Throughput Nucleotide Sequencing
- Data Compression