General Package for State Lab for Carbapenem-resistant Acinetobacter baumannii (CRAB) Detection

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Quick Start Installation

1. Install necessary conda ENV from CRAB.yml file in resources

Only needed for HomeBrew pipeline

  conda env create -f CRAB.yaml

  conda activate CRAB

Before Running update Variables

1. Update necessary locations in Pipeline_Variable.json for your system

Running Analysis

Running PHoeNIx

1. Run [CRAB Runner Script] (scripts/CRAB_Analysis_Runner.py) which takes path to fastq, run date (MMDDYY), pipeline type
2. Make the third argument "CDC"

  python CRAB_Analysis_Runner.py PathToFastq RunDate CDC

See Phoenix Wrapper documentation for more info

Running HomeBrew Pipeline

1. Run CRAB Runner Script which takes path to fastq, run date (MMDDYY)
2. Do not include a third argument if running Homebrew

  python CRAB_Analysis_Runner.py PathToFastq RunDate

Running Phylogenetic Tree Builder

1. Run CRAB Runner Script which takes path to fastq, rundate (MMDDYY)
2. Make the third argument "tree"

  python CRAB_Analysis_Runner.py PathToFastq RunDate tree

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The package contains the following workflows in their respective subdirectories:

Phoenix Launcher: Run CDC Phoenix

• Wrapper to run CDC's PHoeNIx
• Parses and uploads results to internal DB

Workflow 0: Assembley

• Organize sample reads
• Trim and removed low-quality reads
• Assembly reads using SPAdes
• Check assembly quality

This step is required, assembly is needed for downstream analysis.

Workflow 1: Annotate

• Find the Multilocus sequence typing (MLST).
• Annotate genome.

This step is not required but is needed for the final report.

Workflow 2: Find AMR Genes

• Finds antimicrobial resistance genes within the assembled genome
• Parses output

This step is required, to find resistances.

Workflow 3: Database Push

• Open HORIZON LIMS database (Oracle).
• Join all demographics with sample ID.
• Join demographics with assembly stats.
• Create resistance gene table.
• Push new demographics, assembly stats, resistance gene to CRAB DB SQL database.
• Write demographical information for final result file

This step is only required if uploading to a SQL DB.

Workflow 3.5: Phylogenetic Tree and SNP Heat Map

• Takes consensus sequences and creates a SNP heatmap and Phylogenetic Tree

Workflow 4: Create Report

• Creates final report for Epidemiologists
• Summarizes all results