GenomeTools - manual page for GT(1)

## 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 <gt-users@genometools.org>.