This repository contains scripts to run the analyses performed in the methodological paper PanDelos-frags (tool available at InfOmics/PanDelos-frags)
These scripts assume that the tools used are installed and accessible in the current working directory. The tools being compared are PanDelos-frags, Roary, GenAPI, and Panaroo.
Other tools being used in the analysis are Prokka, Diamond, ete3, FastTree, mafft.
In order to run the pangenomic tools, it is required that you have the synthetic data generated by PANPROVA.
These are available in the directories PANPROVA_synth_ecoli/, PANPROVA_synth_myco/, and /PANPROVA_synth_paeru.
Within these directories there are the directories ori which contains info on complete genomes generated by PANPROVA.
The other directories are 0.5., 0.6, 0.7, 0.8, 0.9, and 1, which represent the respective percentage of genome being
virtually sequenced when artificially fragmenting the genomes, and contain the respective fragmented genomes (e.g. genome_9_fr.fasta)
and .log files generated by PANPROVA that are required to extract the genes.
Additionally the survival_families and survival_gene.list files containing information on gene families and genes that are
retained after fragmentation are present.These files correspond to the ground truth gene family composition at different levels of fragmentation.
The script synthetic.sh runs the four tools on these genomes.
Downstream analysis on the resulting pangenomes are performed in the first section of tools_comparison.ipynb and by running the script synthetic_trees.py
The notebook includes analyses on homology relationship, diffusivity, and core genes while the script contains the phylogenetic inference steps.
In our study we consider metagenomic assembled genomes from three species belonging to different phyla that were reconstructed, annotated, and made available online by Pasolli et al. (2019).
Data is downloaded within the analysis scripts, however within the directories abiotrophia_defectiva, bacteroides_nordii, and pseudomonas_aeruginosa there are files containing links
to download the genomes, namely reference.txt for the NCBI RefSeq genome relative to the species and sequence_url_opendata.txt for metagenomic assembled genomes.
The script metagenome.sh runs the four tools on these genomes.
Downstream analysis on the resulting pangenomes are performed in the second section of tools_comparison.ipynb and in process_metagenomes.ipynb
In the first notebook, diffusivity of the four tools is compared, in the second one we show the comparison between PanDelos-frags and Roary.
The directories analysis_scripts/ and panprova_blast_scripts/ contain all the internal scripts called by the main scripts.