odgi break

Break cycles in the graph and drop its paths.


odgi break [-i, --idx=FILE] [-o, --out=FILE] [OPTION]…


The odgi break command finds cycles in a graph via breadth-first search (BFS) and breaks them, also dropping the graph’s paths.



-i, --idx=FILE
Load the succinct variation graph in ODGI format from this FILE. The file name usually ends with .og. It also accepts GFAv1, but the on-the-fly conversion to the ODGI format requires additional time!
-o, --out=FILE
Write the broken graph in ODGI format to FILE. A file ending of .og is recommended.

Cycle Options

-c, --cycle-max-bp=N
The maximum cycle length at which to break (default: 0).
-s, --max-search-bp=N
The maximum search space of each BFS given in number of base pairs (default: 0).
-u, --repeat-up-to=N
Iterate cycle breaking up to N times or stop if no new edges are removed.
-d, --show
Print the edges we would remove to stdout.


-t, --threads=N
Number of threads to use for parallel operations.

Processing Information

-P, --progress
Print information about the operations and the progress to stderr.

Program Information

-h, --help
Print a help message for odgi break.