Analyze 454 flowgrams (.SFF files)
flower - FLOWgram ExtractoR tools
This is now obsolete, please install the biosff library (which includes the flower exectuable) instead.
The flower executable reads files in SFF-format and produces various output, including sequences with quality, or flowgram data in tabular format. By default, it outputs a textual representation of the data in the SFF-file, much like sffinfo from Roche does.
The flowselect executable extracts reads from SFF-files, generating a new SFF-file with a subset of the reads based on various quality criteria.
The flowt program removes (artificial) duplicates from SFF files. It's currently a work in progress, but included if you'd like to play with it. It's faster than other approaches (e.g. CD-HIT), and ought to be more sensitive and specific, but this needs to be proven.