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# gthconsensus(1)
## 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
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