CRAM is a format designed by the European Bioinformatics Institute. See for the EBI's documentation. It uses reference based compression, meaning that only base calls that differ to a designated reference sequence need to be stored.

Typically CRAM achieves 40-50% space saving over the alternative BAM format.

The CRAM specification can be found at the page along with related formats.

Download and Installation

Packages supporting the CRAM format include Samtools/Htslib, Scramble, Cramtools and Picard/Htsjdk. Please download one of those to get support for the file format.


A generic email list is shared for all associated alignment formats at


Sanger Contributors
External Contributors


  • Efficient storage of high throughput DNA sequencing data using reference-based compression.

    Hsi-Yang Fritz M, Leinonen R, Cochrane G and Birney E

    Genome research 2011;21;5;734-40

  • The Scramble conversion tool.

    Bonfield JK

    Bioinformatics (Oxford, England) 2014;30;19;2818-9

Tool Type