SYNOPSIS
gt tirvish [option ...] -index INDEXNAME
DESCRIPTION
-index [string]
- specify the name of the enhanced suffix array index (mandatory) (default: undefined)
-seed [value]
- specify minimum seed length for exact repeats (default: 20)
-mintirlen [value]
- specify minimum length for each TIR (default: 100)
-maxtirlen [value]
- specify maximum length for each TIR (default: 1000)
-mintirdist [value]
- specify minimum distance of TIRs (default: 500)
-maxtirdist [value]
- specify maximum distance of TIRs (default: 10000)
-mat [value]
- specify matchscore for extension-alignment (default: 2)
-mis [value]
- specify mismatchscore for extension-alignment (default: -2)
-ins [value]
- specify insertionscore for extension-alignment (default: -3)
-del [value]
- specify deletionscore for extension-alignment (default: -3)
-xdrop [value]
- specify xdropbelowscore for extension-alignment (default: 5)
-similar [value]
- specify TIR similarity threshold in therange [1..100%] (default: 85.000000)
-overlaps [...]
- specify no|best|longest|all (default: best)
-mintsd [value]
- specify minimum length for each TSD (default: 2)
-maxtsd [value]
- specify maximum length for each TSD (default: 11)
-vic [value]
- specify the number of nucleotides (to the left and to the right) that will be searched for TSDs around 5' and 3' boundary of predicted TIRs (default: 60)
-hmms
- profile HMM models for domain detection (separate by spaces, finish with --) in HMMER3 format Omit this option to disable pHMM search.
-pdomevalcutoff [value]
- global E-value cutoff for pHMM search default 1E-6
-pdomcutoff [...]
- model-specific score cutoff choose from TC (trusted cutoff) | GA (gathering cutoff) | NONE (no cutoffs) (default: GA)
-maxgaplen [value]
- maximal allowed gap size between fragments (in amino acids) when chaining pHMM hits for a protein domain (default: 50)
-refseqs [string]
- specify the name of the gene sequences to scan for inside candidates (default: undefined)
-seqids [yes|no]
- use sequence descriptions instead of sequence numbers in GFF3 output (default: yes)
-md5 [yes|no]
- add MD5 hashes to seqids in GFF3 output (default: no)
-help
- display help for basic options and exit
-help+
- display help for all options and exit
-version
- display version information and exit