Provided by: genometools_1.6.1+ds-2_amd64
gt-shredder - Shredder sequence file(s) into consecutive pieces of random length.
gt shredder [option ...] [sequence_file ...]
-coverage [value] set the number of times the sequence_file is shreddered (default: 1) -minlength [value] set the minimum length of the shreddered fragments (default: 300) -maxlength [value] set the maximum length of the shreddered fragments (default: 700) -overlap [value] set the overlap between consecutive pieces (default: 0) -sample [value] take samples of the generated sequences pieces with the given probability (default: 1.000000) -clipdesc [yes|no] clip descriptions after first space (fooled by \t, \n etc) adds offset and length to ensure unique identifier (default: no) -width [value] set output width for FASTA sequence printing (0 disables formatting) (default: 0) -o [filename] redirect output to specified file (default: undefined) -gzip [yes|no] write gzip compressed output file (default: no) -bzip2 [yes|no] write bzip2 compressed output file (default: no) -force [yes|no] 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 https://github.com/genometools/genometools/issues.