odgi kmers

Display and characterize the kmer space of a graph.

SYNOPSIS

odgi kmers [-i, --idx=FILE] [-c, --stdout] [OPTION]…

DESCRIPTION

Given a kmer length, the odgi kmers command can emit all kmers. The output can be refined by setting the maximum number of furcations at edges or by not considering nodes above a given node degree limit.

OPTIONS

MANDATORY ARGUMENTS

-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!

-k, --kmer-length=N

The kmer length to generate kmers from.

Kmer Options

-c, --stdout

Write the kmers to standard output. Kmers are line-separated.

-e, --max-furcations=N

Break at edges that would induce this many furcations when generating a kmer.

-D, --max-degree=N

Don’t take nodes into account that have a degree greater than N.

Threading

-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 kmers.