Provided by: genometools_1.5.1-2ubuntu1_amd64
gt-shredder - Shredder sequence file(s) into consecutive pieces of random length.
gt shredder [option ...] [sequence_file ...]
-coverage set the number of times the sequence_file is shreddered (default: 1) -minlength set the minimum length of the shreddered fragments (default: 300) -maxlength set the maximum length of the shreddered fragments (default: 700) -overlap set the overlap between consecutive pieces (default: 0) -sample take samples of the generated sequences pieces with the given probability (default: 1.00) -width set output width for FASTA sequence printing (0 disables formatting) (default: 0) -o redirect output to specified file (default: undefined) -gzip write gzip compressed output file (default: no) -bzip2 write bzip2 compressed output file (default: no) -force force writing to output file (default: no) -help display help and exit -version display version information and exit
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 <email@example.com>. 10/07/2012 GT-SHREDDER(1)