PanCons

Description

PanCons aims at assessing genome conservation, based on a pangenome graph.
It is a successor of PanSel, at base level resolution.

Installation

Download the code, and make should do.

Usage

In its simplest form:

pancons -i input.gfa -r reference_name > output.bed 2> output.log

Compulsory parameters:
  -i string: file name in GFA format
  -r string: reference path name (should be in the GFA)
Input specific parameters:
  W-lines specific parameters:
    -p int: if the GFA uses W lines, the reference HapIndex (usually '0' for haploid, default: 0)
    -c int: if the GFA uses W lines, the reference SeqId (usually the chromosome name)
  P-lines specific parameters:
    -c string: if the GFA uses P lines, reference named used in the output BED format
Optional parameters:
  -n float/int: int = min # non-reference paths, float = min fraction of non-reference paths (default: 0.9)
  -z int: max insertion size in nodes (default: 1000)
Other:
  -h: print this help and exit
  -v: print version number to stderr

Input GFA file

The GFA format is not standardized yet. PanSel needs minimal information in order to deduce chromosomes from paths.

The GFA file should not be rGFA, and contain segments (S) and full length paths (P) or walks (W). Other lines are unused.
This GFA can only store one or several chromosomes.
The reference path name should be the second field of a P line (PathName) or a W line (SampleId) in the GFA file.
If the GFA file contains one chromosome, you can provide the name of this chromosome (to appear in the output file) using parameter -c.
If the GFA file contains several chromosomes, only W lines are supported, and the name of the chromosome should be the fourth field (SeqId).

Exemple

If you have a P-line file, and that the second field of the reference file is GCF_019614135.1#1#NZ_CP080645.1, the parameters are:

-r GCF_019614135.1 -p 1 -c NZ_CP080645.1

Output BED file

The output is a BED file, where the last field is the conservation score (0 is not conserved at all, and 1 is totally identical).

Testing PanCons

You can use PancCons on a small sample, provided by the BubbleGun package:

wget -c https://zenodo.org/record/7937947/files/ecoli50.gfa.zst
./pancons -i <( zstd -d -c ecoli50.gfa.zst ) -r GCF_019614135.1 -p 1 -c NZ_CP080645.1 > ecoli.bed 2> ecoli.log

Support

Please contact matthias.zytnicki@inrae.fr for any question you may have.

License

GNU General Public License v3.0.

mzytnicki/pancons