Bifrost YAML Data Collection and Processing

This Python package was developed pipeline to collect, parse, and filter genomic analysis results from Bifrost-generated YAML files. It extracts data related to:

• MLST
• AMR genes
• Plasmids
• Virulence genes
• Point mutations
• QC stampers

Package Structure

data_processing.py

Contains utility functions to:

• Parse YAML outputs from Bifrost
• Filter based on coverage and identity thresholds
• Handle multiple analysis tools: ariba, amrfinderplus, assemblatron, kma_pointmutations, etc.
• Return cleaned results as pandas DataFrames

data_collection.py

Handles:

• Reading a sample sheet (.xlsx)
• Validating sample directories and expected result files
• Calling parsing functions from data_processing
• Aggregating and returning dataframes
• Optional grouping by sample prefixes (e.g., batch/project IDs)

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Installation

Make sure you have Python >3.8 and the required dependencies installed.

To install the package and script locally:

git clone https://github.com/ssi-dk/bifrost_reporter
cd bifrost_reporter
pip install .

Input Requirements

Configuration file

A configuration file in YAML format able to point to the input file Excel sheets listing the Bifrost sample names. The package will scan the dictory where the Excel sheet is stored for

An example of how it is formatted :

project:
    name: "EQA"

Illumina:
    new:  "/xxx/xxx/xxx/sample_sheet.xlsx"
    original:  "/xxx/xxx/xxx/Illumina_original/sample_sheet.xlsx"

Where in this case new are the sample to be compared again original.

Expected YAML Files per Sample

Each sample directory must contain:

• __amrfinderplus_fbi.yaml
• __ariba_resfinder.yaml
• __ariba_virulencefinder.yaml
• __ariba_plasmidfinder.yaml
• __ariba_mlst.yaml
• __assemblatron.yaml
• __kma_pointmutations.yaml
• __ssi_stamper.yaml
• __reslab_stamper.yaml
• (others like __sp_ecoli_fbi.yaml, __whats_my_species.yaml are optional)

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Usage

1. Run the Reporter

The config YAML file specifying paths to your sample sheets:

Illumina:
  new: /path/to/new/samples.xlsx
  original: /path/to/original/samples.xlsx

2. Run the Reporter

Use the installed command-line tool like this:

bifrost_reporter -c config.yaml -l report.log

Arguments

Argument	Description	Required	Default
-c, --config	Path to your configuration YAML file.	Yes	—
-l, --log	Path to your log file.	No	bifrost_results.log