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This is the command gt-readjoiner-assembly that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

PROGRAM:

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 <[email protected]>.

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