Man page - gt-encseq-encode(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-ENCSEQ-ENCODE
NAMESYNOPSIS
DESCRIPTION
REPORTING BUGS
NAME
gt-encseq-encode - Encode sequence files (FASTA/FASTQ, GenBank, EMBL) efficiently.
SYNOPSIS
gt encseq encode sequence_file [sequence_file [sequence_file ...]]
DESCRIPTION
-showstats [ yes|no ]
show compression results (default: no)
-ssp [ yes|no ]
output sequence separator positions to file (default: yes)
-des [ yes|no ]
output sequence descriptions to file (default: yes)
-sds [ yes|no ]
output sequence description separator positions to file (default: yes)
-md5 [ yes|no ]
output MD5 sums to file (default: yes)
-clipdesc [ yes|no ]
clip descriptions after first whitespace (default: no)
-sat [ string ]
specify kind of sequence representation by one of the keywords direct, bytecompress, eqlen, bit, uchar, ushort, uint32 (default: undefined)
-dna [ yes|no ]
input is DNA sequence (default: no)
-protein [ yes|no ]
input is protein sequence (default: no)
-plain [ yes|no ]
process as plain text (default: no)
-dust [ yes|no ]
mask low-complexity regions using the dust algorithm (default: no)
-dustwindow [ value ]
windowsize for the dust algorithm (default: 64)
-dustthreshold [ value ]
threshold for the dust algorithm (default: 2.000000)
-dustlink [ value ]
Max. distance between regions masked by dust before merging. (default: 1)
-indexname [ string ]
specify name for index to be generated (default: undefined)
-smap [ string ]
specify file containing a symbol mapping (default: undefined)
-lossless [ yes|no ]
allow lossless original sequence retrieval (default: no)
-v [ yes|no ]
be verbose (default: no)
-help
display help for basic options and exit
-help+
display help for all options and exit
-version
display version information and exit
REPORTING BUGS
Report bugs to https://github.com/genometools/genometools/issues.