CRAM toolkit 3.0
The CRAM toolkit is a Java program for writing and reading CRAM files. The CRAM format, based on the research paper Efficient storage of high throughput DNA sequencing data using reference-based compression, will be described in detail in a separate specification. Briefly, the CRAM format is based on efficient compression of DNA sequences by storing only differences between aligned and reference sequences with provision for reads that do not map to the reference. The CRAM format is expected to dramatically lower the storage cost for archiving re-sequencing reads.
- Linux / Windows / MacOsX
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Genome Res. 2011 May;21(5):734-40. Epub 2011 Jan 18.
Efficient storage of high throughput DNA sequencing data using reference-based compression.
Hsi-Yang Fritz M, Leinonen R, Cochrane G, Birney E.