gthconsensus1

Usage

Overview

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