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PhyloPHoeNIx was built and is maintained by bioinformatians in the CDC's Division of Healthcare Quality Promotion (DHQP) to standardize surveillance of antibiotic resistance threats, identification of novel resistance threats and support public health laboratories in their genomic analysis of these organisms.
PhyloPHoeNIx is a bioinformatics analysis pipeline built using Nextflow, a workflow management language to run tasks across multiple compute infrastructures in a portable manner. It uses containers for each step making installation trivial and results highly reproducible. PhyloPHoeNIx is meant to be used in combination with DHQP's 🔥🐦🔥 PHoeNIx as it takes as input a PHoeNIx style output directory or samplesheet with the location of samples that have already be run through PHoeNIx. Both pipelines are designed for use with pathogens causing healthcare-associated bacterial infections. PhyloPHoeNIx is a comprehensive pipeline that performs:
- Automation of DHQP's iterative outbreak analysis (runs analysis on all samples and when --by_st is passed also separates isolates by ST and runs each group through the analysis).
- SNV (single-nucleotide variant) matrix creation
- Phylogenetic tree building
- Reports the % core genome used the SNV determination
The use of PhyloPHoeNIx and PHoeNIx together provide a standardized approach for identifying, characterizing and tracking potential relatedness of healthcare-associated bacterial pathogens, specifically for public health partners. DHQP supports CDC’s Antimicrobial Resistance Laboratory Network (AR Lab Network) mission to rapidly detect emerging and novel antimicrobial resistance threats. PhyloPHoeNIx was developed to advance these objectives. Specifically, it is meant to seamlessly integrate with its companion pipeline, PHoeNIx (Portable Healthcare Nextgen Informatics pipeline). PHoeNIx analysis includes quality control, assembly, taxonomic identification, sequence typing (MLST), plasmid replicons, antimicrobial resistance gene identification, and hypervirulence gene identification.
CDC’s Antimicrobial Resistance Laboratory Network (AR Lab Network) mission is to rapidly detect emerging and novel antimicrobial resistance threats. PhyloPHoeNIx was developed to advance these objectives. Specifically, it is meant to seamlessly integrate with its companion pipeline, PHoeNIx (Portable Healthcare Nextgen Informatics pipeline). PHoeNIx analysis includes quality control, assembly, taxonomic identification, sequence typing (MLST), plasmid replicons, antimicrobial resistance gene identification, and hypervirulence gene identification.
PhyloPHoeNIx generates several files that are compatible with downstream visualization tools like Microreact. This pipeline is currently only available to run on CLI, but in the future support for Terra, Nextflow tower, and Illumina Connect Analysis will be added. Broad distribution of this tool will enhance both local public health capacity and national efficiency in utilizing whole genome sequencing (WGS) data for healthcare-associated infection (HAI) surveillance and investigation.
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. Like PHoeNIx, PhyloPHoeNIx is a bioinformatics analysis pipeline built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a portable manner. It uses 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.
We highly encourage collaboration and welcome feedback on DHQP’s 🔥🌿🐦🔥 PhyloPHoeNIx pipeline. However, if you choose to fork the code, you are assuming responsibility for that new fork. The DHQP Clinical and Environmental Microbiology Branch does not guarantee the performance or results of any pipelines or scripts that have been forked or copied from this repo.
Credits:
- Jill Hagey @jvhagey
- Nick Vlachos @nvlachos
- Thao Masters @masters-thao
- Alyssa Kent @Alyssa-Kent
At the heart of this pipeline is a program called SNVPhyl written by Aaron Petkau (@apetkau). There are stand-alone versions of SNVPhyl written for Nextflow, Galaxy, and WDL. For documentation on SNVPhyl see the following links.