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.