CRAM

CRAM is a more highly compressed alternative to the BAM and SAM DNA sequence alignment file formats.

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

See http://www.ebi.ac.uk/ena/software/cram-toolkit for the EBI’s documentation. Typically CRAM achieves 40-50% space saving over the alternative BAM format. The CRAM specification can be found at the http://samtools.github.io/hts-specs/ page along with related formats.

Downloads

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.

Contact

If you need help or have any queries, please contact us using the details below.

A generic email list is shared for all associated alignment formats at samtools-help@lists.sourceforge.net or use the tool specific github pages for submitting issues.


Sanger Institute Contributors

Photo of James Bonfield

James Bonfield

Principal Software Developer

External Contributor

Photo of Vadim Zalunin

Vadim Zalunin

EMBL-EBI

 
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