NovCor Manuscript

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.

See NovCor_Manuscript for the rendered version of the code and analysis notebooks, which are organized by method and analysis type.

The data/ folder contains all the files related to the analyses performed for the manuscript. The main analyses include:

• 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 species 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.

• Most relevant data relative to construction of phylogenetic and phylogenomic trees:

  • 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.