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3. SFF Tools Commands
3.
SFF Tools Commands
3.1 sfffile
3.2 sffinfo
3.3 sff2scf
3.4 fnafile
3.5 sffrescore
The 454 Sequencing System Software package contains five programs related to the handling of Standard Flowgram Format (SFF) files or other read data. These programs allow you to:
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combine files into the Standard Flowgram Format (SFF) and filter reads present in SFF files [sfffile]
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access SFF file information [sffinfo]
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dynamically generate an SCF trace file suitable for display by the consed software [sff2scf]
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prepare FASTA files with the necessary annotations for use by the GS De Novo Assembler and GS Reference Mapper [fnafile]
•
rescore older SFF files (generated with software versions prior to v. 1.1.03) using the new phred-based quality scores [sffrescore]
These tools are all evoked from the Linux command line. The descriptions below assume that the reader is familiar with the GS Junior and GS FLX+ Systems data and formats, including the SFF file format. For more details on the SFF and other file formats used in the 454 Sequencing System software, see the General Overview section of this manual.