odgi unitig

Output unitigs of the graph.

SYNOPSIS

odgi unitig [-i, --idx=FILE] [OPTION]…

DESCRIPTION

The odgi unitig command can print all unitigs of a given odgi graph to standard output in FASTA format. Unitigs can also be emitted in a fixed sequence quality FASTQ format. Various parameters can refine the unitigs to print.

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!

FASTQ Options

-f, --fake-fastq

Write the unitigs in FASTQ format to stdout with a fixed quality value of I.

Unitig Options

-t, --sample-to=N

Continue unitigs with a random walk in the graph so that they have at least the given N length.

-p, --sample-plus=N

Continue unitigs with a random walk in the graph by N past their natural end.

-l, --min-begin-node-length=N

Only begin unitigs collection from nodes which have at least length N.

Processing Information

-P, --progress

Print information about the operations and the progress to stderr.

Program Information

-h, --help

Print a help message for odgi extract.

Program Information

-h, --help

Print a help message for odgi unitig.