Codes i wrote for the paper "genomic resources for Mediterranean fishes"

to adjust an old reference genome

Aphrocallistes vastus genome

Bioinformatics pipeline written in bash for annotating and obtaining the 5 genes of the rabies virus.

Comprehensive three-way consensus annotation pipeline for Giardia genomes (v5.0)

Script suite for generating and analyzing synthetic DNA

Arche: a flexible tool for annotation of prokaryotic contigs

Code accompanying the manuscript on Genome variation in alpine bumblebees.

Scripts to index and align Bovine genome with HISAT2

Code of the article that describes the molecular epidemiology analyses of OsHV-1 virus by whole genome sequencing approaches in French shellfish growing areas.

Genomics Part of the KAUST High Throughput Sequencing Workshop 2019

Polap is a plant mtDNA assembly pipeline using Flye long-read assembler guided by organelle gene annotation.

Teaching Material for Course "Computational Bioscience & Machine Learning 2021 - Genome Assembly"

Detecting transposable element invasions without repeat library. Detects also horizontal transfer events and endogenized viruses. All you need is a reference genome and some short reads

Run multiple metagenome filtering programs using Docker containers

Methods for genome paper

Whole genome sequence simulation of DUF1220 domains and testing of alignment strategies

SARS-CoV-2 Genome Assembler

A ToolKit to perform a Meta-analysis of Genome-Wide Association Studies

Script to infer the reference genome from a VCF