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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:

-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)

display help and exit

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 <gt-users@genometools.org>.

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