Another common use of sfffile is to extract subsets of the reads from a sequencing Run or a set of sequencing Runs, to perform further processing. Using the –i and –e options, one can construct an SFF file containing only the reads of interest, and then use that for further processing, e.g. input it into to the GS
De Novo Assembler or GS Reference Mapper applications. For example, a user can extract the singletons from an assembly (when performing, say, survey sequencing) by executing the following commands (which assume that the current working directory is the output directory of the assembly):
Or, after running the GS Reference Mapper application, you can retrieve the reads that did not map to your reference sequence (so that, for example, you can give them as input to the GS De Novo Assembler software to see if there are any contigs that are part of what you sequenced but are not part of the reference) by using the following commands (which assume that the current working directory is the output directory of the assembly):
