odgi bin

binning of pangenome sequence and path information in the graph

SYNOPSIS

odgi bin [-i, –idx=FILE] [OPTION]…

DESCRIPTION

The odgi bin(1) command bins a given variation graph. The pangenome sequence, the one-time traversal of all nodes from smallest to largest node identifier, can be summed up into bins of a specified size. For each bin, the path metainformation is summarized. This enables a summarized view of gigabase scale graphs. Each step of a path is a bin and connected to its next bin via a link. A link has a start bin identifier and an end bin identifier.

The concept of odgi bin is also applied in odgi viz. A demonstration of how the odgi bin JSON output can be used for an interactive visualization is realized in the Pantograph project. Per default, odgi bin writes the bins to stdout in a tab-delimited format: path.name, path.prefix, path.suffix, bin (bin identifier), mean.cov (mean coverage of the path in this bin), mean.inv (mean inversion rate of this path in this bin), mean.pos (mean nucleotide position of this path in this bin), first.nucl (first nucleotide position of this path in this bin), last.nucl (last nucleotide position of this path in this bin). These nucleotide ranges might span positions that are not present in the bin. Example: A range of 1-100 means that the first nucleotide has position 1 and the last has position 100, but nucleotide 45 could be located in another bin. For an exact positional output, please specify [-j, –json].

Running odgi bin in HaploBlocker mode, only arguments [-b, –haplo-blocker], [-p[N], –haplo-blocker-min-paths[N]], and [-c[N], –haplo-blocker-min-coverage[N]] are required. A TSV is printed to stdout: Each row corresponds to a node. Each column corresponds to a path. Each value is the coverage of a specific node of a specific path.

OPTIONS

Graph Files IO

-i, –idx=FILE

File containing the succinct variation graph to investigate the bin from. The file name usually ends with .og.

FASTA Options

-f, –fasta=FILE

Write the pangenome sequence to FILE in FASTA format.

Bin Options

-n, –number-bins=N

The number of bins the pangenome sequence should be chopped up to.

-w, –bin-width=N

The bin width specifies the size of each bin.

-D, –path-delim=STRING

Annotate rows by prefix and suffix of this delimiter.

-a, –aggregate-delim

Aggregate on path prefix delimiter. Argument depends on [-D, –path-delim=STRING].

-j, –json

Print bins and links to stdout in pseudo JSON format. Each line is a valid JSON object, but the whole file is not a valid JSON! First, each bin including its pangenome sequence is printed to stdout per line. Second, for each path in the graph, its traversed bins including metainformation: bin (bin identifier), mean.cov (mean coverage of the path in this bin), mean.inv (mean inversion rate of this path in this bin), mean.pos (mean nucleotide position of this path in this bin), and an array of ranges determining the nucleotide position of the path in this bin. Switching first and last nucleotide in a range represents a complement reverse orientation of that particular sequence.

-s, –no-seqs

If [-j, –json] is set, no nucleotide sequences will be printed to stdout in order to save disk space.

-g, –no-gap-links

We divide links into 2 classes:

1. the links which help to follow complex variations. They need to be drawn, else one could not follow the sequence of a path.

2. the links helping to follow simple variations. These links are called gap-links. Such links solely connecting a path from left to right may not be relevant to understand a path’s traversal through the bins. Therefore, when this option is set, the gap-links are left out saving disk space

HaploBlocker Options

-b, –haplo-blocker

Write a TSV to stdout formatted in a way ready for HaploBlocker: Each row corresponds to a node. Each column corresponds to a path. Each value is the coverage of a specific node of a specific path.

-p[N], –haplo-blocker-min-paths[N]

Specify the minimum number of paths that need to be present in the bin to actually report that bin. The default value is 1.

-c[N], –haplo-blocker-min-coverage[N]

Specify the minimum coverage a path needs to have in a bin to actually report that bin. The default value is 1.

Program Information

-h, –help

Print a help message for odgi bin.

-P, –progress

Write the current progress to stderr.