CRAM

CRAM is a file format for the lossless compression of sequence data. CRAM files are often used in bioinformatics and genomics, where they are used to store large amounts of data in a compact form. The CRAM format is designed to be efficient, both in terms of storage space and computational resources, and is capable of storing data in a way that is both flexible and scalable.

Overview

The CRAM format was developed by the European Bioinformatics Institute (EBI) as a way to efficiently store and retrieve large amounts of sequence data. The format uses a combination of compression techniques, including Huffman coding, run-length encoding, and delta encoding, to reduce the size of the data. In addition to these standard compression techniques, CRAM also uses a reference-based compression scheme, where the sequence data is stored as differences from a reference sequence.

Features

One of the key features of the CRAM format is its use of reference-based compression. This means that instead of storing the entire sequence data, only the differences from a reference sequence are stored. This can significantly reduce the size of the data, especially for large genomes where the majority of the sequence is identical to the reference.

Another important feature of the CRAM format is its flexibility. The format allows for the storage of a wide range of data types, including sequence data, quality scores, and alignment information. This makes it suitable for a wide range of applications in bioinformatics and genomics.

Applications

The CRAM format is widely used in bioinformatics and genomics, where it is used to store and retrieve large amounts of sequence data. It is particularly useful in situations where storage space is at a premium, such as in cloud computing environments or on portable devices.

See also

• Bioinformatics
• Genomics
• Data compression
• File format

References

CRAM Resources
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