odgi crush

Crush runs of N.

SYNOPSIS

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

DESCRIPTION

Replaces runs of Ns with single Ns (for example, ANNNT becomes ANT).

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!

-o, --out=FILE

Write the N-crushed succinct variation graph in ODGI format to FILE. A file ending of .og is recommended.

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 crush.