jwirth/phantasm repository overview

⁠PHANTASM: PHylogenomic ANalyses for the TAxonomy and Systematics of Microbes

⁠Developed by Joseph S. Wirth

⁠Source code is available at https://github.com/dr-joe-wirth/phantasm⁠

⁠If you use our software, please cite our paper

Automating microbial taxonomy workflows with PHANTASM: PHylogenomic ANalyses for the TAxonomy and Systematics of Microbes

Joseph S. Wirth & Eliot C. Bush, 2023

doi: 10.1093/nar/gkad196⁠ ‎

⁠Note: PHANTASM requires an email address for communicating with NCBI as described in python's Bio.Entrez⁠ package. The email address is not stored or used for any other purposes.

⁠Note: PHANTASM does not always run properly with the current version of podman (3.4.7). It is unclear what is causing this issue.

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⁠A detailed tutorial can be found here⁠

⁠Getting started

⁠Getting the docker image

docker pull jwirth/phantasm:latest

⁠Getting help

docker run -v $(pwd):/data jwirth/phantasm:latest phantasm help

⁠Using Singularity instead of Docker

PHANTASM can be containerized using Singularity. See the detailed tutorial⁠ for more information

⁠Running PHANTASM

⁠Option 1: unknown reference genomes and unknown phylogenetic marker(s)

docker run -v $(pwd):/data jwirth/phantasm:latest phantasm getPhyloMarker -i <input> -e <email address>

Examine initialAnalysis/putativePhylogeneticMarkers; pick one or more phylogenetic markers

docker run -v $(pwd):/data jwirth/phantasm:latest phantasm refinePhylogeny -i <input> -t <locus tag(s)> -e <email address>

⁠Option 2: unknown reference genomes and known phylogenetic marker(s)

docker run -v $(pwd):/data jwirth/phantasm:latest phantasm knownPhyloMarker -i <input> -t <locus tag(s)> -e <email address>

⁠Option 3: known reference genomes

Make a human map file as described in section 3.3⁠ of the tutorial

docker run -v $(pwd):/data jwirth/phantasm:latest phantasm analyzeGenomes -i <input> -m <map file> -e <email address>

⁠Option 4: ranking phylogenetic markers

This only works after running either option 2 or option 3

docker run -v $(pwd):/data jwirth/phantasm:latest phantasm rankPhyloMarkers -i <phantasm results directory>

⁠Analyzing the results

The following files are likely to be the most useful for phylogenomic and taxonomic analyses:

• speciesTree.nwk: this is the species tree, it is rooted on the outgroup, and the outgroup is present in the tree
• speciesTree_outgroupPruned.nwk: this is the same species tree as above, but the outgroup has been pruned to allow better resolution of the relevant phylogenomic relationships
• aai_matrix.txt: this is a raw text file containing the average amino acid identities for all of the taxa in speciesTree_outgroupPruned.nwk
• aai_heatmap.pdf: this is a visualization of the data in aai_matrix.txt and the taxa are ordered to match the order of the taxa in speciesTree_outgroupPruned.nwk. Due to a bug in the R package gplots, the tree cannot be plotted alongside the heatmap at this time.
• ani_matrix.txt: this is a raw text file containing the average nucleotide identities for all of the taxa in speciesTree_outgroupPruned.nwk
• ani_heatmap.pdf: this is a visualization of the data in ani_matrix.txt and the taxa are ordered to match the order of the taxa in speciesTree_outgroupPruned.nwk. Due to a bug in the R package gplots, the tree cannot be plotted alongside the heatmap at this time.
• coreGenesSummary.txt: this is a tab-delimited file containing detailed information on the core genes used to construct the species tree. Locus tags, gene numbers, gene names, and annotations are only specified for the input genomes. The indicated alignment file can be used to determine these data for other reference genomes used in the analysis.
• wgsHumanMap.txt: this file lists all of the accession numbers for the genomes used in the analysis as well as their human readable names found in the alignments, trees, and heatmaps. The equivalent of this file was provided by the user if analyzeGenomes was used.