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gt-shredder - Online in the Cloud

Run gt-shredder in OnWorks free hosting provider over Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

This is the command gt-shredder that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

PROGRAM:

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 <[email protected]>.

Use gt-shredder online using onworks.net services


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