odgi explode

Breaks a graph into connected components storing each component in its own file.

SYNOPSIS

odgi explode [-i, --idx=FILE] [-p, –prefix=STRING] [OPTION]…

DESCRIPTION

The odgi explode command breaks a graph into connected components, writing each component in its own file.

OPTIONS

MANDATORY OPTIONS

-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!

Explode Options

-g, --to-gfa

Write each connected component to a file in GFAv1 format.

-p, --prefix=STRING

Write each connected component in a file with the given STRING prefix. The file for the component number i will be named STRING.i.EXTENSION

(default: component.i.og or component.i.gfa).

-b, --biggest=N

Specify the number of the biggest connected components to write, sorted by decreasing size (default: disabled, for writing them all).

-s, --sorting-criteria=C
Specify how to sort the connected components by size:
p) Path mass (total number of path bases) (default).
l) Graph length (number of node bases).
n) Number of nodes.
P) Longest path.

-O, --optimize

Compact the node ID space in each connected component.

Threading

-t, --threads=N

Number of threads to use for parallel operations.

Processing Information

-P, --progress

Print information about the components and the progress to stderr.

Program Information

-h, --help

Print a help message for odgi explode.