NAME

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

SYNOPSIS

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

OPTIONS

       -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

DESCRIPTION

       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

AUTHOR

       Report bugs to <gt-users@genometools.org>.

                                            10/07/2012                             GT-SHREDDER(1)