odgi flatten

Generate linearizations of a graph.

SYNOPSIS

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

DESCRIPTION

The odgi flatten command projects the graph sequence and paths into FASTA and BED.

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!

Output Options

-f, --fasta=FILE

Write the concatenated node sequences in FASTA format to FILE.

-n, --name-seq=STRING

The name to use for the concatenated graph sequence. Default is the name of the input file which was specified via [-i, --idx=FILE].

-b, --bed=FILE

Write the mapping between graph paths and the linearized FASTA sequence in BED format to FILE.

Threading

-t, --threads=N

Number of threads to use (to embed the subpaths in parallel).

Processing Information

-P, --progress

Print information about the operations and the progress to stderr.

Program Information

-h, --help

Print a help message for odgi flatten.