Using sfffile for Evaluation of Individual Reads

3.1.1

One of the most common uses of the sfffile program is to collect and organize your sequences in terms of a user’s projects, instead of the standard timestamp- and Run-based organization generated by the GS Junior and GS FLX+ Instruments. For example, multiple sff files can easily be combined into a single “mygenome.sff” file using

sfffile ‑o mygenome.sff

     path_to_file1.sffpath_to_file2.sffpath_to_file3.sff

This file could then be given to the GS De Novo Assembler and GS Reference Mapper software, or carved and divided into separate pieces (see below), while still preserving the traceback information to the source data, since:

•	The universal accessions for each read encode the Run timestamp, the region and the X,Y location of the read, and all but ensure uniqueness for the accessions.

•

The manifest of the SFF file provides the mapping from the Run prefix of the universal accessions to the actual Run and Data Processing directories used to generate the read. When universal accessions are given to the reads, the manifest is kept updated through multiple invocations of sfffile (as best it can).

Thus, if a particular read needs investigation, the user can invoke the sffinfo command (see section 3.2, below) for that read to see the traceback information, including the source Run and Data Processing directories. The GS Run Browser (see Part B of this Reference Manual) could be used to evaluate the read within the context of the Run [where the Find location feature on the Wells tab allows entry of a universal accession and will then center the image and place a marker at the read’s X,Y location].