gt - The GenomeTools genome analysis system.
gt [option ...] [tool | script] [argument ...]
-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".
Report bugs to
https://github.com/genometools/genometools/issues.