Société Française de Bioinformatique

Mots-Clés

pangenomics nanopore

Description

From Nanopore Sequencing to Pangenome Analysis of Bacterial Genomes

Background
This internship aims to explore the genomic diversity within two bacterial genus: Pectobacterium and Erwinia, using pangenomic approaches.
The student will begin by reviewing existing tools for constructing, analyzing, and visualizing pangenomes. Based on this review, the most suitable tool will be selected to address scientific questions and assist researchers in extracting and interpreting data from the generated pangenomes.
The pangenomes will be built using both publicly available datasets and proprietary data generated via Nanopore sequencing.

The internship will be structured in three phases:
1. Genomic Data Collection
* Identify and retrieve public genomic datasets
* Integrate private data (Nanopore assemblies and gene annotations)
2. Pangenome Construction
3. Data Exploration and Analysis
* Identify core and accessory genes
* Visualize synteny
* Perform phylogenetic analyses & extract MLSA markers

Main Objectives
* Develop a pipeline for assembling and annotating bacterial genomes from Nanopore data
* Evaluate and compare existing pangenomic tools
* Understand and address scientific questions through pangenome analysis
* Build a pangenome using selected tools
* Develop modules to query and extract relevant data from the pangenome
* Support scientists in exploring and interpreting pangenomic data
* Present findings and methodologies

Requirements
* Proficiency in English (spoken and written)
* Programming experience in Bash, R, and/or Python
* Comfortable working in a Linux environment