SffReadsQ class is a container for storing, next-generation sequencing read data, read id, and sequencing quality information imported directly from SFF files generated by technologies such as Roche 454 and Life Sciences Ion Torrent. This class provides a way to store and manipulate, in a coordinated fashion, next generation reads stored in SFF files, their identifiers and quality scores.
Clip modes are used to store "views" on the sequence object. They are often used to identify adapter sequences and low-quality "ends" which will be trimmed before further analysis. Storing clipping information instead of clipped sequences is useful for avoiding loss of data while maintaining information about the appropriate nucleotides for down-stream analysis. Each clip mode defines a set of left and right clip points, one set for each read. Clip points are typically included in the SFF file, are generated by the sequence provider and are loaded into the appropriate IRanges object when the SFF file is loaded via readSff. The vendor-generated clip points are not always desireable however, so accomidations for custom clip points are also provided.
Base classes, functions, and methods for representation of high-throughput sequencing data stored in SFF files (such as Roche 454 Data and Life Sciences Ion Torrent). Implementation defined according to http://www.ncbi.nlm.nih.gov/Traces/trace.cgi?cmd=show&f=formats&m=doc&s=formats#sff
readSff
(Package: rSFFreader) :
Read SFF-formatted files into SffReads or SffReadsQ objects
readSff reads all sff files specified in filenames, returning an R object of type SffReads or SffReadsQ which acts and behaves similarly to the ShortRead and ShortReadQ classes from package ShortRead
providing 
.