3. SFF Tools Commands
: 3.5 sffrescore
3.5
sffrescore
The sffrescore command can be used to rewrite existing SFF files with the new Phred-like quality scores. It recursively searches through a list of files or directories, identifies all the SFF files, determines which SFF files contain the older quality scores, runs the sfffile command (with the –r option) to generate a new SFF file with the new quality scores, then overwrites the existing SFF file with the new file. The effect is that the reads, flowgrams and basecalls in the files are left unchanged, but the files now contain new quality scores.
The sffrescore command uses the following syntax:
sffrescore [-f] (file | directory)...
Command
Description
sffrescore
The sffrescore command recursively searches through a list of files or directories, and rescores any SFF file that contains the older quality scores. Any file rescored is rewritten in place with a new version of the SFF file.
Option / Argument
Description
-f
This option forces the rescoring of all SFF files (by default, any SFF file found to already have the new scores are not rewritten).
file or
directory...
List of the files and directories to be processed. The command will recursively search through the directories to find all of the SFF files in the directory trees.
