Man page - gt-shredder(1)
Packages contains this manual
- gt-readjoiner(1)
- gt-cds(1)
- gt-extractfeat(1)
- gt-dupfeat(1)
- gt-select(1)
- gt-encseq(1)
- gt-matstat(1)
- gt-md5_to_id(1)
- gt-seqmutate(1)
- gt-seqtranslate(1)
- gt-mkfeatureindex(1)
- gt-dot(1)
- gt-compreads-decompress(1)
- gt-compreads-refcompress(1)
- gt-condenseq(1)
- gt-readjoiner-prefilter(1)
- gt-seqstat(1)
- gt-readjoiner-overlap(1)
- gt-splicesiteinfo(1)
- gt-prebwt(1)
- gt-extractseq(1)
- gt-encseq2spm(1)
- gt-convertseq(1)
- gt-clean(1)
- gt-encseq-encode(1)
- gt-ltrclustering(1)
- gt-seq(1)
- gt-ltrharvest(1)
- gt-sequniq(1)
- gt-inlineseq_split(1)
- gt-mergefeat(1)
- gt-splitfasta(1)
- gt-gtf_to_gff3(1)
- gt-ltrdigest(1)
- gt-seqfilter(1)
- gt-featureindex(1)
- gt-inlineseq_add(1)
- gt-speck(1)
- gt-mmapandread(1)
- gt-tallymer-mkindex(1)
- gt-seed_extend(1)
- gt-hop(1)
- gt-sketch(1)
- gt-repfind(1)
- gt-shulengthdist(1)
- gt-sketch_page(1)
- gt-gff3(1)
- gt-stat(1)
- gt-gff3validator(1)
- gt-packedindex(1)
- gt-merge(1)
- gt-wtree(1)
- gt-encseq-bitextract(1)
- gt-seqids(1)
- gt-readjoiner-assembly(1)
- gt-tirvish(1)
- gt-uniquesub(1)
- gt-encseq-sample(1)
- gt-chseqids(1)
- gt-compreads-compress(1)
- gt-scriptfilter(1)
- gt-seqtransform(1)
- gt-eval(1)
- gt-genomediff(1)
- gt-congruence(1)
- gt-chain2dim(1)
- gt-tallymer(1)
- gt-tagerator(1)
- gt-loccheck(1)
- gt-encseq-info(1)
- gt-snpper(1)
- gt-bed_to_gff3(1)
- gt(1)
- gt-matchtool(1)
- gt-simreads(1)
- gt-csa(1)
- gt-tallymer-occratio(1)
- gt-encseq-check(1)
- gt-tallymer-search(1)
- gt-encseq-bench(1)
- gt-shredder(1)
- gt-gff3_to_gtf(1)
- gt-orffinder(1)
- gt-encseq-decode(1)
- gt-compreads(1)
- gt-encseq-md5(1)
- gt-uniq(1)
- gt-congruence-spacedseed(1)
- gt-id_to_md5(1)
- gt-seqorder(1)
- gt-compreads-refdecompress(1)
- gt-fingerprint(1)
- gt-fastq_sample(1)
- gt-interfeat(1)
apt-get install genometools
Manual
GT-SHREDDER
NAMESYNOPSIS
DESCRIPTION
EXAMPLES:
REPORTING BUGS
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.