gt - Online in the Cloud

PROGRAM:

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 <[email protected]>.

Use gt online using onworks.net services