Man page - gt(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
NAMESYNOPSIS
DESCRIPTION
REPORTING BUGS
NAME
gt - The GenomeTools genome analysis system.
SYNOPSIS
gt [option ...] [tool | script] [argument ...]
DESCRIPTION
-i [ yes|no ]
enter interactive mode after executing tool or script
-q [ yes|no ]
suppress warnings
-test [ yes|no ]
perform unit tests and exit
-seed [ value ]
set seed for random number generator manually. 0 generates a seed from current time and process id
-help
display help and exit
-version
display version information and exit
Tools:
• bed_to_gff3
• cds
• chain2dim
• chseqids
• clean
• compreads
• condenseq
• congruence
• convertseq
• csa
• dot
• dupfeat
• encseq
• encseq2spm
• eval
• extractfeat
• extractseq
• fastq_sample
• featureindex
• fingerprint
• genomediff
• gff3
• gff3_to_gtf
• gff3validator
• gtf_to_gff3
• hop
• id_to_md5
• inlineseq_add
• inlineseq_split
• interfeat
• loccheck
• ltrclustering
• ltrdigest
• ltrharvest
• matchtool
• matstat
• md5_to_id
• merge
• mergefeat
• mgth
• mkfeatureindex
• mkfmindex
• mmapandread
• orffinder
• packedindex
• prebwt
• readjoiner
• repfind
• scriptfilter
• seed_extend
• select
• seq
• seqfilter
• seqids
• seqmutate
• seqorder
• seqstat
• seqtransform
• seqtranslate
• sequniq
• shredder
• shulengthdist
• simreads
• sketch
• sketch_page
• snpper
• speck
• splicesiteinfo
• splitfasta
• stat
• suffixerator
• tagerator
• tallymer
• tirvish
• uniq
• uniquesub
• wtree
Set the environment variable GT_MEM_BOOKKEEPING=on to enable memory bookkeeping (e.g., like this: env GT_MEM_BOOKKEEPING=on gt).
Set the environment variable GT_ENV_OPTIONS=-spacepeak to show a spacepeak after program run. Set the environment variable GT_ENV_OPTIONS=-showtime to show processing times for some program parts if implemented.
Set the environment variable GT_SEED to an integer value to supply a seed for the random number generator. Can be overridden by the -seed option.
Combinations are possible. Running the gt binary with GT_ENV_OPTIONS=-help shows all possible "environment options".
REPORTING BUGS
Report bugs to https://github.com/genometools/genometools/issues.