odgi prune¶
remove complex parts of the graph
SYNOPSIS¶
odgi prune [-i, –idx=FILE] [-o, –out=FILE] [OPTION]…
DESCRIPTION¶
The odgi prune(1) 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¶
Graph Files IO¶
-i, –idx=FILE
File containing the succinct variation graph to load in. The file name
usually ends with .og.
-o, –out=FILE
Write the pruned graph to FILE. The file name should end with .og.
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 nodese 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=N
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.
Path Options¶
-D, –drop-paths
Remove the paths from the graph.
Threading¶
-t, –threads=N
Number of threads to use.
Program Information¶
-h, –help
Print a help message for odgi prune.