gt-shredder - Shredder sequence file(s) into consecutive pieces of random length.
gt shredder [option ...] [sequence_file ...]
Each sequence given in sequence_file is shreddered into consecutive pieces of random length (between -minlength and -maxlength) until it is consumed. By this means the last shreddered fragment of a given sequence can be shorter than the argument to option -minlength. To get rid of such fragments use gt seqfilter (see example below).
Shredder a given BAC:
$ gt shredder U89959_genomic.fas > fragments.fas
Shredder an EST collection into pieces between 50 and 100 bp and get rid of all (terminal) fragments shorter than 50 bp:
$ gt shredder -minlength 50 -maxlength 100 U89959_ests.fas \
| gt seqfilter -minlength 50 - > fragments.fas # 130 out of 1260 sequences have been removed (10.317%)
Shredder an EST collection and show only random 10% of the resulting fragments:
$ gt shredder -sample 0.1 U89959_ests.fas
Report bugs to https://github.com/genometools/genometools/issues.