---
name: "gt"
section: "1"
platform: "linux"
package: "genometools"
version: "1.6.5+ds-2.2"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/gt"
---

# gt(1)

The GenomeTools genome analysis system.

## 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.