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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


Report bugs to <gt-users@genometools.org>.

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