Paper Workflow and Data Repository

This repository contains all data files, scripts, and high-quality figure PDFs necessary to reproduce the analyses and visualizations in the paper: KoSCAPEbio differentiates species of the Klebsiella oxytoca Complex in 16S rRNA Amplicon Data. Each folder corresponds to a specific figure in the paper, containing the data and scripts used to generate the results. Additionally, high-quality PDFs of the figures are provided use in the publication.

Repository Organization

Main Folders and Figures

• Figure_1/: Contains all data and scripts used to generate Figure 1, Supplementary Figure S1 and Supplementary Figure S5 related to Phylogeny analysis.
  Contents: csv, fasta, nwk, txt, tsv, py

• Figure_2/: Contains all data and scripts used to generate Figure 2 and Supplementary Figure S6, both related to Alignment.
  Contents: fasta, nwk, txt, py

• Figure_3/: Contains all data and scripts used to generate Figure 3 related to the Mock-16S dataset.
  Contents: fasta, qza, png, tsv, biom, aln, fastq, py, sh

• Figure_4/: Contains all scripts used to generate Figure 4 related to the Mock-WGS dataset.
  Contents: R

• Figure_5/: Contains all data and scripts used to generate Figure 5, related to Clinical Datasets.
  Contents: fasta, qza, tsv, txt, png, biom

• Figure_6/: Contains all data and scripts used to generate Figure 6 and Supplementary Figure S7, related to Sim Clinical Dataset.
  Contents: R

• Figure_7/: Contains all data and scripts used to generate Figure 7, related to Odds Ratio - NEC.
  Contents: R

Supplementary Figures without Dedicated Folder

• No Folder:
  • Supplementary Figure S2: Pipeline Database
  • Supplementary Figure S3: Pipeline Search
  • Supplementary Figure S4: Datasets overlap

PDFs

• PDFs/: High-quality PDF versions of Figures 1–7 and Supplementary Figures S1–S7 used in the publication.

Excel

• Excel/: Contains all raw data required for reproducibility, organized into four separate .xlsx files:
  • Supplementary_file_1.xlsx – Tables S1–S8 for Figures 1 and 2
  • Supplementary_file_2.xlsx – Tables S9–S14 for Figures 3 and 4
  • Supplementary_file_3.xlsx – Tables S15–S24 for Figures 5 and 6
  • Supplementary_file_4.xlsx – Tables S25–S27 for Figure 7

Reproducing Figures

The folders for each figure contain the relevant data and scripts needed for analysis and visualization. Each script is labeled according to what it does.

1. Install Required Software: Ensure you have the necessary software installed, such as Python or R, along with any specific libraries used in the scripts. Requirements are noted within each script.

2. Adjust Paths as Needed:

   • Absolute file paths (e.g., working directory paths) have been omitted from the scripts for privacy reasons. Before running the scripts, please set the working directory or update file paths as needed to match the locations of the downloaded data on your system.

3. Run Scripts:

   • Navigate to the appropriate Figure_* folder for the figure you wish to replicate.
   • Run the scripts to process the data and generate the figure components.

4. PDF Access: High-resolution PDFs of each figure are available in the PDFs/ folder.

Citation

If you use this repository, please cite our paper:

Refining Microbiome Resolution: KoSCAPEbio Identifies Klebsiella oxytoca Complex Species in 16S rRNA Amplicon Data and Uncovers Associations with NEC
Authors: Amar Cosic, Bettina Halwachs, Kristina Schild, Ellen L. Zechner, & Sabine Kienesberger Journal: [Journal Name, Year]
DOI: [DOI or link to paper]

Contact

For help and support, please contact:

• Name: Amar Cosic
• Email: amar.cosic995@gmail.com