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.