gt (1)

gt [option ...] [tool | script] [argument ...]

-i [yes|no]

enter interactive mode after executing tool or script (default: no)

-test [yes|no]

perform unit tests and exit (default: no)

-seed [value]

set seed for random number generator manually 0 generates a seed from current time and process id (default: 473885254)

-help

display help and exit

-version

display version information and exit

Tools:

bed_to_gff3

cds

chain2dim

chseqids

clean

compreads

condenser

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

interfeat

loccheck

ltrclustering

ltrdigest

ltrharvest

matchtool

matstat

md5_to_id

merge

mergefeat

mgth

mkfeatureindex

mkfmindex

mmapandread

orffinder

packedindex

prebwt

readjoiner

repfind

scriptfilter

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 <[email protected]>.