Mots-Clés

virus nextflow workflow web hpc genomics omics

Description

Start date: December 2026 – March 2027 (flexible)

Context

The CIRI is a research unit (INSERM, CNRS, Université Lyon 1, ENS de Lyon) spanning Virology, Bacteriology, and Immunology.

This internship is a collaboration between the Ibiv team (Dr. Olivier Reynard) and the Bioinformatics Hub (Dr. Julien Fouret). The goal is to deploy a reusable web interface enabling biologists to submit HPC workloads on the local PSMN-ENS Lyon infrastructure, centered on a viral metagenomics pipeline and complemented by in-house exploration tools.

The Ibiv team studies emerging zoonotic viruses, notably bat-associated Paramyxoviridae (Henipaviruses). Dr. Reynard recently received ANR funding to investigate Parahenipaviruses identified in French shrews — close relatives of bat viruses. Objectives: characterize genetic diversity, assess prevalence in wild populations, and identify viruses with pathogenic potential, all essential for zoonotic preparedness.

The Bioinformatics Hub’s mission is to democratize bioinformatics across CIRI teams. With limited human resources, it invests in training and interactive tool deployment. This internship delivers a solution tailored to Dr. Reynard’s needs, designed for reuse across teams. The hub has already initiated a Flask web app nf-web and selected and integrated the nf-core/viralmetagenome pipeline.

Co-supervision: Olivier Reynard (product owner) / Julien Fouret (technical lead).

Missions

1. Explore and valorize the nf-core/viralmetagenome outputs

Understand the full analytical output: QC reads, host-depleted reads, de novo and reference-guided viral assemblies, contig taxonomic classification (Kraken2/BLAST), read mapping statistics, consensus sequences.

Build an interactive exploration interface (Shiny or Dash) providing:

• Interactive filtering of BLAST results (reads and contigs)
• Taxonomic composition plots (Krona-like, Sankey)
• Viral contig coverage depth visualizations
• Assembly quality metrics (N50, GC content, CheckV completeness)

2. Complementary downstream analyses and extension workflows

Implement a secondary analysis pipeline (Nextflow or post-processing modules):

• Terminal-sequence re-assembly via iterative mapping — refining genome ends by successive read-mapping/extension rounds, critical for paramyxovirus leader/trailer regions missed by standard assemblers
• Targeted reannotation using curated paramyxovirus protein databases (P/V/C, F, HN, N, L) to refine gene boundaries and detect P-gene editing sites, alternative ORFs, and F protein cleavage motifs

3. Extend the web application for HPC submission

The existing Flask app already provides:

• Workflow selection with version pinning
• HPC configuration (partition, CPU/memory/time, Singularity/Apptainer container paths)
• Dynamic parameterization via JSON schema-driven forms (nf-schema): sample sheets, reference genomes, database indices, with data-portal file picker links

You will extend it with:

• Run launching with pre-flight validation (schema compliance, input existence) and run resume support
• Real-time run management: streaming Nextflow logs, per-task resource metrics, failure diagnostics
• Run dashboard: summary statistics and direct links to outputs

Data transfer: integrate a PSMN-hosted solution or a FileZilla-based approach for uploading/downloading sequencing files (fastq/fasta) and metadata tables.

Desired skills & knowledge

All the stack is not required, the intern will be trained on what he is not familiar with.

• Viral genomics: read preprocessing (trimming, QC, host depletion), assembly challenges (repeats, circular genomes, low termini coverage), mapping and consensus (minimap2, Bowtie2, iVar, bcftools)
• HPC & workflows: SLURM, SSH remote work, Nextflow in HPC, Singularity/Apptainer
• Web development: Flask (Python), asynchronous task execution
• DevOps: Git; Ansible and CI/CD exposure appreciated
• Interactive visualization: R Shiny or Python Dash/Streamlit for genomic data
• UI/UX: intuitive interfaces for non-bioinformaticians; form logic, error messaging, data provenance