CRAM
Download
The CRAM Java toolkit can be downloaded as follows:
CRAM 2.0 current production toolkit
CRAM 2.0 is also supported in beta in the latest Staden io_lib package.
Format specification
The CRAM format specification is available as follows:
CRAM 2.0 current production specification
CRAM 1.0 previous specification
For detailed infromation about the preservation data from source BAM data in CRAM format please refer to ArchiveCRAM 1.0 specification.
Overview
CRAM is a framework technology comprising file format and toolkit in which we combine highly efficient and tunable reference-based compression of sequence data with a data format that is directly available for computational use. In support of CRAM, we also provide the CRAM reference registry.
Building on early proof-of-principle for reference-based compression (Hsi-Yang Fritz,et al. (2011)Genome Res. 21:734-740), our approach has been to balance usability with compression efficiency.
CRAM supports production pipelines for the European Nucleotide Archive*. Current work includes improvements to functionality and broader integration with third party tools.
We remain involved in the community discussion around the application of CRAM to different types of data (Cochrane G.et al. (2012).GigaScience1:2)
The latest CRAM version is the CRAM 2.0. Please note that minor revisions to the format are possible during the two month review period.
More information about the CRAM Java toolkit is available here.
Our principles for CRAM development are available, usage instructions are presented here and we encourage membership of the CRAM developers mailing list.