gt-readjoiner-assembly - Construct string graph and output contigs.

-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

       gt-readjoiner-assembly - Construct string graph and output contigs.

       Report bugs to https://github.com/genometools/genometools/issues.

GenomeTools 1.6.5                                  04/27/2024                              GT-READJOINER-ASSE(1)

gtreadjoinerassembly [option ...]