Salmonella Typhimurium screen identifies shifts in mixed acid fermentation during gut colonization

Analysis with mBARq

• We have set up small snakemake pipeline to use for data analysis with mBARq.

1. Pre-process Illumina short read data using standard workflow.

2. Map libraries to reference genome using mbarq map command.

rbseq map -c rbseq_workflow/configs/28-06-23-mapping-config.yaml

3. Count the barcodes across samples using mbarq count command.

rbseq merge -c rbseq_workflow/configs/03-08-23-counting-config.yaml 

4. Perform differential abundance analysis using mbarq analyze command.

rbseq analyze -c rbseq_workflow/configs/03-08-23-counting-config.yaml

5. Explore. All of the data generated at each step of the worklow is available for download and further exploration through mBARq app.

Data Analysis

• All of the code used to generate figures for the paper can be found in code/notebooks/08-23-rbtnseq-analysis.ipynb.
• The data needed to run the notebook is in code/notebooks/nguyen.tar.gz archive. Run tar -xzvf code/notebooks/nguyen.tar.gz to extract the archive and make sure the root in code/notebooks/nguyenb_config.yaml is pointing to the extracted folder.
• Packages required to run the notebook are listed in code/notebooks/env.yaml.