Description of Corynebacterium nasorum sp. nov. and Corynebacterium hallucis sp. nov. isolated from human nasal passages and skin

Authors

Tommy Tran

Isabel Fernandez Escapa

Published

April 2, 2026

Introduction

This repository contains the code and main analysis files used for bioinformatics and data analysis for the manuscript “Description of Corynebacterium nasorum sp. nov. and Corynebacterium hallucis sp. nov. isolated from human nasal passages and skin”.

A preprint of this manuscript is available at bioRxiv.

The data/ folder contains all the files related to the analyses performed for the manuscript and is available at this GitHub repository

Repository structure

Code for the custom Prokka annotations can be found in here.
- The data/genomes folder contains the original .fasta files for all genomes used in the analysis, organized in subfolders based on the figures they were used for.
- The data/genome_lists folder contains the lists of genomes used for different analyses, including the 28 proposed C. nasorum genomes and the 30 genomes representative of the C. tuberculostearicum complex.
Detailed code for the ANI and dDDH analysis.
- The data/pyani-plus folder contains the results from the ANI analysis.
- The data/GGDC folder contains the results from the dDDH analysis.
All the code used for construction of phylogenetic and phylogenomic trees is summarized here.
- The data/phylogenies folder contains all the files related to phylogenetic and phylogenomic analyses, including alignments and tree files.
Analysis performed using anvi’o is documented in here.
- The data/anvio-9 folder contains all the files related to anvi’o analyses, including contigs databases, metabolic analysis, and pangenome analysis.

# Introduction {.unnumbered .unlisted}

This repository contains the code and main analysis files used for bioinformatics and data analysis for the manuscript **"Description of *Corynebacterium nasorum* sp. nov. and *Corynebacterium hallucis* sp. nov. isolated from human nasal passages and skin"**.

A preprint of this manuscript is available at [bioRxiv](https://www.biorxiv.org/content/10.1101/2024.11.21.624533v1).

The `data/` folder contains all the files related to the analyses performed for the manuscript and is available at [this GitHub repository](https://github.com/KLemonLab/NovCor_Manuscript)

## Repository structure

-   Code for the custom Prokka annotations can be found in [here](https://klemonlab.github.io/NovCor_Manuscript/Methods_Prokka_Annotations.html).

    -   The `data/genomes` folder contains the original `.fasta` files for all genomes used in the analysis, organized in subfolders based on the figures they were used for.
    
    -   The `data/genome_lists` folder contains the lists of genomes used for different analyses, including the 28 proposed *C. nasorum* genomes and the 30 genomes representative of the *C. tuberculostearicum* complex.

-   Detailed code for the [ANI](https://klemonlab.github.io/NovCor_Manuscript/Methods_ANIs.html) and [dDDH](https://klemonlab.github.io/NovCor_Manuscript/Methods_dDDH.html) analysis.

    -   The `data/pyani-plus` folder contains the results from the ANI analysis.

    -   The `data/GGDC` folder contains the results from the dDDH analysis.

-   All the code used for construction of phylogenetic and phylogenomic trees is summarized [here](https://klemonlab.github.io/NovCor_Manuscript/Methods_Phylogenies.html).

    -   The `data/phylogenies` folder contains all the files related to phylogenetic and phylogenomic analyses, including alignments and tree files.

-   Analysis performed using anvi'o is documented in [here](https://klemonlab.github.io/NovCor_Manuscript/Methods_Anvio.html).

    -   The `data/anvio-9` folder contains all the files related to anvi'o analyses, including contigs databases, metabolic analysis, and pangenome analysis.