---
name: "gthconsensus"
section: "1"
platform: "linux"
package: "genomethreader"
version: "1.7.3+dfsg-10+b1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/gthconsensus"
---

# gthconsensus(1)

build consensus spliced alignments

## NAME

gthconsensus - build consensus spliced alignments

## SYNOPSIS

**gthconsensus** \[option ...\] \[file ...\]

## DESCRIPTION

Show GenomeThreader output files containing intermediate results and assemble the contained spliced alignments to consensus spliced alignments.

## OPTIONS

- **-translationtable**

  set the codon translation table used for codon translation in matching, DP, and output default: 1

- **-v**

  be verbose default: no

- **-xmlout**

  show output in XML format default: no

- **-gff3out**

  show output in GFF3 format default: no

- **-md5ids**

  show MD5 fingerprints as sequence IDs default: no

- **-o**

  redirect output to specified file default: undefined

- **-gzip**

  write gzip compressed output file default: no

- **-bzip2**

  write bzip2 compressed output file default: no

- **-force**

  force writing to output file default: no

- **-gs2out**

  output in old GeneSeqer2 format default: no

- **-minalignmentscore**

  set the minimum alignment score for spliced alignments to be included into the set of spliced alignments default: 0.00

- **-maxalignmentscore**

  set the maximum alignment score for spliced alignments to be included into the set of spliced alignments default: 1.00

- **-mincoverage**

  set the minimum coverage for spliced alignments to be included into the set of spliced alignments default: 0.00

- **-maxcoverage**

  set the maximum coverage for spliced alignments to be included into the set of spliced alignments default: 9999.99

- **-intermediate**

  stop after calculation of spliced alignments and output results in reusable XML format. Do not process this output yourself, use the \`\`normal'' XML output instead! default: no

- **-help**

  display help for basic options and exit

- **-help+**

  display help for all options and exit

- **-version**

  display version information and exit