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