odgi flatten

Generate linearizations of a graph.


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


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



-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.


-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.