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.