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Compression of SCF Files

The SCF format version 3.00 has been designed with file compression in mind. No new information is recorded when compared to the version 2.02 format, except the data is stored in a manner conducive to efficient compression.

Experimentation (1) has shown that 16 bit SCF version 3.00 files can achieve a 9:1 compression ratio and 8 bit SCF files a 14.5:1 compression ratio. These figures are for SCF files without quality values compressed using the bzip utility. gzip tends to give between 20 to 40% larger files than bzip. Compressed SCF files containing accuracy values tend to be around 10% larger than those without accuracy values.

Whilst compression is not a specific part of the SCF standard, the size of trace files and the compression ratios attainable suggests that it is wise to handle compressed files. The Staden Package utilities, such as gap4 and Trev, automatically uncompress and compress SCF files as needed.


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This page is maintained by James Bonfield. Last generated on 2 Febuary 1999.
URL: http://www.mrc-lmb.cam.ac.uk/pubseq/manual/formats_10.html