sffinfo

3.2

The sffinfo command extracts read information from an SFF file, and reports it in text form. It can be used for generating the FASTA and quality score files of the read sequences, which can be given to standard bioinformatics tools. The sffinfo command uses the following syntax:

sffinfo [options...] [- | sfffile] [accno...]

Command	Description
sffinfo	The sffinfo command extracts read information from an SFF file, and reports it in text form. By default, a text summary of all the read information is output, but the output can be limited to only the sequences, quality scores, flowgrams or manifest. All output is written to standard output. If trimming occurs, sffinfo will exclude zero-length reads from the output.

Option / Argument	Description
-a or -accno	This option limits the output to only the accession numbers.
-s or -seq	This option limits the output to only the sequences.
-q or -qual	This option limits the output to only the quality scores.
-f or -flow	This option limits the output to only the flowgrams.
-t or -tab	The default format for the sequences, quality scores and flowgram is FASTA. This option changes this to tab-delimited lines.
-n or -notrim	By default, the trimmed data is output. The -notrim option changes this to output the untrimmed sequences or quality scores.
-m or -mft	The command does not output the manifest by default. This option outputs the manifest text, if it exists in the SFF file. In this case, the -tab and -notrim options and the accnos on the command line are ignored.
[--help]	Displays a usage line and short description of the command.
[--version]	Displays the current software version of the command.
- \| sfffile	Path to the SFF file whose data will be output. If this is replaced by a “-” on the command line, then standard input is read for the SFF contents.
accno...	List of the accession numbers of the reads whose data will be output. If no accnos are given on the command line, the information from all reads in the file are output. If an SFF file is specified and it contains an sfffile-created index, then an index-based lookup is used and the reads are output in the order they appear on the command line. If not, the complete SFF file is scanned and the reads are output in the order they appear in the file.

Only one of -accno, -seq, -qual, -flow or -mft may be specified: the program uses the last one specified on the command line.