gt-readjoiner-assembly1
Construct string graph and output contigs.
Usage
gt readjoiner
assembly
[option ...]
Overview
-
-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
Releases
6 releases since Debian 8 (Jessie); the text changed 5 times.