Scroll to navigation

GT(1) GenomeTools Manual 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 https://github.com/genometools/genometools/issues.

04/27/2024 GenomeTools 1.6.5