This section introduces the various file formats used by the package, but first we describe some limitations on the names of files. There are restrictions on the characters used in file names and the length of the file names. Characters permitted in file names: QWERTYUIOPASDFGHJKLZXCVBNMqwertyuiopasdfghjklzxcvbnm1234567890._- A reading name or experiment file name used in a sequence assembly project must not be longer than 16 characters. These restrictions also apply to SCF files which means, in turn, also to the names given to samples obtained from sequencing instruments. For example do not give sample names such as 27/OCT/96/r.1 when using and ABI machine: the / symbols will be interpreted as directory name separators on UNIX!
Currently the formats used by the package include the following.