odgi kmers¶
show and characterize the kmer space of the graph
SYNOPSIS¶
odgi kmers [-i, –idx=FILE] [-c, –stdout] [OPTION]…
DESCRIPTION¶
Given a kmer length, the odgi kmers(1) 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¶
Graph Files IO¶
-i, –idx=FILE
File containing the succinct variation graph to convert from. The file
name usually ends with .og.
-c, –stdout=
Write the kmers to standard output. Kmers are line-separated.
Kmer Options¶
-k, –kmer-length=N
The kmer length to generate kmers from.
-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.
Program Information¶
-h, –help
Print a help message for odgi kmers.