NAME

       gt-shredder - Shredder sequence file(s) into consecutive pieces of random length.

SYNOPSIS

       gt shredder [option ...] [sequence_file ...]

DESCRIPTION

       -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).

EXAMPLES:

       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

REPORTING BUGS

       Report bugs to https://github.com/genometools/genometools/issues.