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Welcome to the PHoeNIx 🔥🐦🔥 wiki!

PHoeNIx is a bioinformatics analysis pipeline built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The Nextflow DSL 2 implementation of this pipeline uses one container per process which makes it easier to maintain and update software dependencies. Where possible, these processes have been submitted to and installed from nf-core/modules in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community!

PHoeNIx takes in Illumina paired-end reads and was designed for use with pathogens causing healthcare-associated bacterial infections. This comprehensive pipeline performs:

• Quality control
• Checks for contamination
• Confirms taxa ID
• Performs sequence typing
• Assembles reads into scaffolds
• Detects antibiotic resistance and hypervirulence genes
• Searches for plasmid markers

PHoeNIx generates several files that are compatible with downstream analytic tools, such as those used for phylogenetic tree-building. PHoeNIx was developed to support bioinformatics capacity in public health laboratories. This pipeline will be available to run on Terra (coming Fall 2022), Nextflow tower, CLI and will be incorporated into the StaPH-B toolkit (coming Fall 2022). Broad distribution of this tool will enhance both local public health capacity and national efficiency in utilizing WGS data for healthcare-associated infection (HAI) surveillance and investigation.

This pipeline was developed in the Division of Healthcare Quality Promotion (DHQP) at the CDC. If you require assistance, please contact the DHQP Clinical and Environmental Microbiology Branch (CEMB) at [email protected]. You can also contact us in the Slack #phoenix-dev channel.

Credits:

• Maria Diaz @MzDiaz824
• Nick Vlachos @nvlachos
• Jill Hagey @jvhagey
• Rich Stanton @astanton
• Alyssa Kent @alyssagkent