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".