nf-core pipeline ·
nf-core/pathogenepidemiology
A profile-based Nextflow pipeline for genomic epidemiological analysis of predefined pathogens.
What nf-core/pathogenepidemiology is
nf-core/pathogenepidemiology is a bioinformatics workflow designed for genomic epidemiology investigations of predefined pathogens. It uses a profile-based strategy to evaluate pathogen genomic sequences alongside host contexts.
The software is developed within the nf-core community by Igiraneza Clement, Bilal Asser, Firas Zemzem, and other contributors. It addresses the need for structured, reproducible analyses when tracking and characterising infectious disease agents.
What the pipeline does
The pipeline ingests sequencing reads alongside reference genomes for both the pathogen of interest and its host. Processing includes quality control of raw reads using FastQC, followed by aggregate quality control reporting using MultiQC.
Key facts
- Pipeline engine
- Nextflow
- Development status
- Under development
- Core authors
- Igiraneza Clement, Bilal Asser, Firas Zemzem
- Included tools
- FastQC, MultiQC
- Required inputs
- Sequencing samplesheet, pathogen reference genome, host reference genome
What you can use it for
- Pathogen read quality assessment
- Assessing the sequencing quality of raw reads using FastQC and inspecting compiled MultiQC reports before epidemiological analysis.
- Genomic epidemiology with host-pathogen systems
- Analysing predefined pathogen genomes in the context of their respective hosts, such as Plasmodium falciparum and Anopheles gambiae.
Run it here
The research agent runs nf-core/pathogenepidemiology with Nextflow on its own machine — up to 32 cores, 256 GiB of memory and 24 hours per run, which covers the test profile and real single-sample runs. It builds the samplesheet, checks it against the pipeline's schema and reads the results back. When a run is too big for one machine, it gives you the exact command for your own cluster instead.
Strengths and limits
Good at
- Built within the community-curated nf-core framework for reproducible Nextflow analyses.
- Supports dual reference setups incorporating both host and pathogen reference genomes.
- Includes standard automated quality control using FastQC and MultiQC.
Watch out for
- The pipeline is explicitly marked as under development and its feature set is not yet finalised.
- Requires reference genomes for both the target pathogen and the host organism.
Questions
Can I run nf-core/pathogenepidemiology without my own cluster?
The research agent runs nf-core/pathogenepidemiology with Nextflow on its own machine — up to 32 cores, 256 GiB of memory and 24 hours per run, which covers the test profile and real single-sample runs. It builds the samplesheet, checks it against the pipeline's schema and reads the results back. When a run is too big for one machine, it gives you the exact command for your own cluster instead.
What licence is nf-core/pathogenepidemiology under?
MIT, like every nf-core pipeline.
What reference genomes are needed to run the pipeline?
The pipeline requires reference genome FASTA files for both the pathogen of interest and its host.
Which quality control tools are included?
The pipeline runs FastQC for raw read quality checks and MultiQC to generate summary reports.
What is the development status of nf-core/pathogenepidemiology?
It is currently under active development.
How to cite it
Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen. The nf-core framework for community-curated bioinformatics pipelines. Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.
Written from nf-core/pathogenepidemiology's own README. Statements citing a figure that does not appear there are removed before publication. Licence and running details come from our registry.