odgi normalize

Compact unitigs and simplify redundant furcations.

SYNOPSIS

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

The odgi normalize command unchops odgi unchop a given variation graph and simplifies redundant furcations.

-i, --idx=FILE

Load the succinct variation graph in ODGI format from this FILE. The file name usually ends with .og.

-o, --out=FILE

Write the normalized dynamic succinct variation graph in ODGI format to this file. A file ending with .og is recommended.

-I, --max-iterations=N

Iterate the normalization up to N many times. The default is 10.

-t, --threads=N

Number of threads to use for parallel operations.

-d, --debug

Print information about the normalization process to stdout.

-P, --progress

Print information about the operations and the progress to stderr.

-h, --help

Print a help message for odgi normalize.