CRAM

CRAM

CRAM

Overview

CRAM is a format designed by the European Bioinformatics Institute. See http://www.ebi.ac.uk/ena/software/cram-toolkit 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 http://samtools.github.io/hts-specs/ 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.

Contact

A generic email list is shared for all associated alignment formats at samtools-help@lists.sourceforge.net

Authors

Sanger Contributors
External Contributors

Publications

  • 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