CRAM (file format)

CRAM
Filename extension
.cram
Developed byMarkus Hsi-Yang Fritz et al; Vadim Zalunin; James Bonfield
Type of formatBioinformatics
Open format?yes
Websitewww.ga4gh.org/cram/, www.ebi.ac.uk/ena/software/cram-toolkit

Compressed Reference-oriented Alignment Map (CRAM) is a compressed columnar file format for storing biological sequences aligned to a reference sequence, initially devised by Markus Hsi-Yang Fritz et al.[1]

CRAM was designed to be an efficient reference-based alternative to the Sequence Alignment Map (SAM) and Binary Alignment Map (BAM) file formats. It optionally uses a genomic reference to describe differences between the aligned sequence fragments and the reference sequence, reducing storage costs. Additionally each column in the SAM format is separated into its own blocks, improving compression ratio. CRAM files typically vary from 30 to 60% smaller than BAM, depending on the data held within them.

Implementations of CRAM exist in htsjdk,[2] htslib,[3] JBrowse,[4] and Scramble.[5]

The file format specification is maintained by the Global Alliance for Genomics and Health (GA4GH)[6] with the specification document available from the EBI cram toolkit page.[7]

  1. ^ Hsi-Yang Fritz, Markus; Leinonen, Rasko; Cochrane, Guy; Birney, Ewan (May 2011). "Efficient storage of high throughput DNA sequencing data using reference-based compression". Genome Research. 21 (5): 734–740. doi:10.1101/gr.114819.110. ISSN 1549-5469. PMC 3083090. PMID 21245279.
  2. ^ "Htsjdk by Broad Institute". samtools.github.io. Retrieved 2018-10-14.
  3. ^ "Samtools". www.htslib.org. Retrieved 2018-10-14.
  4. ^ "JBrowse · A fast, embeddable genome browser built with HTML5 and JavaScript". jbrowse.org. Retrieved 2018-10-14.
  5. ^ Bonfield, James K. (2014-06-14). "The Scramble conversion tool". Bioinformatics. 30 (19): 2818–2819. doi:10.1093/bioinformatics/btu390. ISSN 1460-2059. PMC 4173023. PMID 24930138.
  6. ^ "GA4GH". www.ga4gh.org. Retrieved 2018-10-14.
  7. ^ EMBL-EBI. "CRAM toolkit < Software < European Nucleotide Archive < EMBL-EBI". www.ebi.ac.uk. Retrieved 2018-10-14.