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 <gt-users@genometools.org>.