NAME
gt-readjoiner-assembly - Construct string graph and output contigs.
SYNOPSIS
gt readjoiner assembly [option …]
DESCRIPTION
- -readset [string]
-
specify the readset name (default: undefined)
- -spmfiles [value]
-
number of SPM files to read this must be equal to the value of -j for the overlap phase (default: 1)
- -l [value]
-
specify the minimum SPM length (default: 0)
- -depthcutoff [value]
-
specify the minimal number of nodes in a contig (default: 3)
- -lengthcutoff [value]
-
specify the minimal length of a contig (default: 100)
- -errors [yes|no]
-
search graph features which may originate from sequencing errors and remove them (default: no)
- -bubble [value]
-
number of rounds of p-bubble removal to perform (default: 3)
- -deadend [value]
-
number of rounds of dead end removal to perform a dead end (default: 10)
- -deadend-depth [value]
-
specify the maximal depth of a path to an end-vertex by which the path shall be considered a dead end (default: 10)
- -v [yes|no]
-
be verbose (default: no)
- -q [yes|no]
-
suppress standard output messages (default: no)
- -help
-
display help for basic options and exit
- -help+
-
display help for all options and exit
- -version
-
display version information and exit
REPORTING BUGS
Report bugs to https://github.com/genometools/genometools/issues.