odgi prune

Remove parts of the graph.

SYNOPSIS

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

DESCRIPTION

The odgi prune command can remove complex parts of a graph. One can drop paths, nodes by a certain kind of edge coverage, edges and graph tips. Specifying a kmer length and a maximum number of furcations, the graph can be broken at edges not fitting into these conditions.

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 pruned graph in ODGI format to FILE. A file ending with .og is recommended.

Kmer Options

-k, --kmer-length=N
The length of the kmers to consider.
-e, --max-furcations=N
Break at edges that would induce N many furcations in a kmer.

Node Options

-d, --max-degree=N
Remove nodes that have a higher node degree than N.
-c, --min-coverage=N
Remove nodes covered by fewer than N number of path steps.
-C, --max-coverage=N
Remove nodes covered by more than N number of path steps.
-T, --cut-tips
Remove nodes which are graph tips.

Edge Options

-E, --edge-coverage
Remove edges outside of the minimum and maximum coverage rather than nodes. Only set this argument in combination with [-c, –min-coverage=N] and [-C, --max-coverage=N].
-b, --best-edges=N
Only keep the N most covered inbound and output edges of each node.

Step Options

-s, --expand-steps=N
Also include nodes within this many steps of a component passing the prune thresholds.
-l, --expand-length=N
Also include nodes within this graph nucleotide distance of a component passing the prune thresholds.

Path Options

-p, --expand-path-length=N
Also include nodes within this path length of a component passing the prune thresholds.
-r, --drop-paths=FILE
List of paths to remove. The FILE must contain one path name per line and a subset of all paths can be specified.
-D, --drop-all-paths
Remove all paths from the graph.
-y, --drop-empty-paths
Remove empty paths from the graph.
-m, --cut-tips-min-depth=N
Remove nodes which are graph tips and have less than N path depth.
-I, --remove-isolated
Remove isolated nodes covered by a single path.

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 prune.