PanExplorer_workflow

About

This workflow is a snakemake worklow that can be run in the backend of the PanExplorer web application.

Homepage: https://panexplorer.southgreen.fr/

It allows to perform a pan-genome analysis using published and annotated bacteria genomes, using different tools that can be invoked: Roary, PGAP, PanACoTA.

It provides a presence/absence matrix of genes, an UpsetR Diagram for synthetizing the matrix information and a COG assignation summary for each strain.

Citation

https://doi.org/10.1093/bioinformatics/btac504

Authors

Alexis Dereeper (IRD)

Prerequisites - Tool dependencies

Using a singularity container, the only dependency you will need is singularity.

This singularity image (panexplorer.sif) already contains all dependencies required for running the workflow:

Snakemake
Roary
PGAP
Panaroo
Panacota
Minigraph/cactus
PanGenome Graph Builder (PGGB)
ncbi-blast+ (version BLAST 2.4.0+)
R (version 4.2.0) and following packages:
- optparse : install.packages("optparse")
- dendextend : install.packages("dendextend")
- svglite : install.packages("svglite")
- heatmaply : install.packages("heatmaply")
- gplots : install.packages("gplots")
- UpSetR : install.packages("UpSetR")

Install

1- Git clone

git clone https://github.com/SouthGreenPlatform/PanExplorer_workflow.git

2- Define the PANEX_PATH environnement variable

cd PanExplorer_workflow
export PANEX_PATH=$PWD

3- Get preformatted RPS-BLAST+ database of the CDD COG distribution

wget https://ftp.ncbi.nlm.nih.gov/pub/mmdb/cdd/little_endian/Cog_LE.tar.gz
tar -xzvf Cog_LE.tar.gz -C $PANEX_PATH/COG

4- Get the singularity container

wget -P $PANEX_PATH/singularity https://panexplorer.southgreen.fr/singularity/panexplorer.sif

Prepare your list of genomes to be analyzed

Edit the configuration file config.yaml to list the Genbank identifiers of complete assembled and annotated genomes.

#########################################################
# Complete one of the following input data
# Remove the other lines if not needed
#########################################################

# Genbank accessions of assembly accession (GCA, GCF)
ids:
  - GCA_001042775.1
  - GCA_001021915.1
  - GCA_022406815.1

# Path of genbank files
input_genbanks:
  - data/GCA_001518895.1.gb
  - data/GCA_001746615.1.gb
  - data/GCA_003382895.1.gb

# Input genomes as fasta and annotation files in GFF format
# Only applied when using Orthofinder or PGGB workflows, starting from fasta and GFF
# To be used preferentially for eukaryotes
input_genomes:
  "MSU7":
    "fasta": "/share/banks/Oryza/sativa/japonica/MSU7/all.con"
    "gff3": "/share/banks/Oryza/sativa/japonica/MSU7/all.gff3"
    "name": "MSU7"
  "kitaake":
    "fasta": "/share/banks/Oryza/sativa/japonica/kitaake/Oryza_sativa_japonica_Kitaake.assembly.fna"
    "gff3": "/share/banks/Oryza/sativa/japonica/kitaake/Oryza_sativa_japonica_Kitaake.gff3"
    "name": "kitaake"
  "nivara":
    "fasta": "/share/banks/Oryza/nivara/Oryza_nivara.assembly.fna"
    "gff3": "/share/banks/Oryza/nivara/Oryza_nivara.gff3"
    "name": "nivara"

It's best not to mix NCBI genomes with your own annotated genomes, to avoid biaises due to annotation method/software. Keep an homogeneous annotation procedure to feed the workflow.

Run the workflow

For prokaryotes

Creating a pangenome using Roary

singularity exec $PANEX_PATH/singularity/panexplorer.sif snakemake --cores 1 -s $PANEX_PATH/Snakemake_files/Snakefile_wget_roary_heatmap_upset_COG

Creating a pangenome using PanACoTA

singularity exec $PANEX_PATH/singularity/panexplorer.sif snakemake --cores 1 -s $PANEX_PATH/Snakemake_files/Snakefile_wget_panacota_heatmap_upset_COG

Creating a pangenome graph using Minigraph/Cactus and derived pangenes matrix

singularity exec $PANEX_PATH/singularity/panexplorer.sif snakemake --cores 1 -s $PANEX_PATH/Snakemake_files/Snakefile_wget_cactus_heatmap_upset_COG

Creating a pangenome graph using PanGenomeGraph Builder (PGGB) and derived pangenes matrix

singularity exec $PANEX_PATH/singularity/panexplorer.sif snakemake --cores 1 -s $PANEX_PATH/Snakemake_files/Snakefile_wget_pggb_heatmap_upset_COG

For eukaryotes

Creating a pangenome using Orthofinder

singularity exec $PANEX_PATH/singularity/panexplorer.sif snakemake --cores 1 -s $PANEX_PATH/Snakemake_files/Snakefile_orthofinder_heatmap_upset

Graphical outputs

In all cases, you should a new directory named "outputs" containing all output files.

In case of a pangenome graph analysis with PGGB, you will obtain vizualizations of the graph (using ODGI)

2D graph visualization : outputs/pggb_out/all_genomes.fa.lay.draw.png
1D graph visualization : outputs/pggb_out/all_genomes.fa.og.viz_multiqc.png

In all cases, it also includes:

ANI (Average Nucleotide Identity) : outputs/fastani.out.svg

The heatmap chart generated from distances calculated based on the ANI values. ANI values are calcultaed using FastANI software.

Presence/absence matrix of accessory genes: outputs/heatmap.svg.complete.new.svg

Both gene clusters and samples have been ordered using a Hierarchical Clustering.

Upset plot: outputs/upsetr.svg

An Upset plot is an alternative to the Venn Diagram used to deal with more than 3 sets. The total size of each set is represented on the left barplot. Every possible intersection is represented by the bottom plot, and their occurence is shown on the top barplot. Each row corresponds to a possible intersection: the filled-in cells show which set is part of an intersection.

Rarefaction curve: outputs/rarefaction_curves.svg

The rarefaction curve (computed by micropan R package) is the cumulative number of gene clusters we can observe as more and more genomes are being considered.

License

GNU General Public GPLv3 License

SouthGreenPlatform / PanExplorer_workflow

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