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


gt readjoiner assembly [option …]


-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)


display help for basic options and exit


display help for all options and exit


display version information and exit