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.