Infectious Diseases and Vectors: Ecology, Genetics, Evolution and Control

The aims of the group MIVEGEC are to develop integrative and transdisciplinary research to the mechanisms that maintain, amplify and transmit pathogenic agents, along with their genetic and epigenetic determinants, in order to better understand how these systems evolve and to improve their control.
L’UMR MIVEGEC "Maladies Infectieuses et Vecteurs : Ecologie, Génétique, Evolution et Contrôle" a pour mission de comprendre, via des recherches intégratives et transdisciplinaires, les mécanismes de maintenance, d’amplification et de transmission d’agents pathogènes, leurs déterminants génétiques et non génétiques, afin de pouvoir mieux appréhender l’évolution de ces systèmes infectieux et contribuer à en améliorer le contrôle.
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Replication Data for: The genome of the avian malaria parasite Haemoproteus majoris (lineage WW2) and its relationship to other Plasmodium species
Replication Data for: The genome of the avian malaria parasite Haemoproteus majoris (lineage WW2) and its relationship to other Plasmodium species
Aug 5, 2026
Bardil, Amélie; Berthomieu, Arnaud; Dainat, Jacques; Fontaine, Michael; Hellgren, Olof; Rivero, Ana; Otto, Thomas; Gandon, Sylvain, 2026, "Replication Data for: The genome of the avian malaria parasite Haemoproteus majoris (lineage WW2) and its relationship to other Plasmodium species", https://doi.org/10.23708/0QPMON, DataSuds, V1
Data and script supporting the paper: "The genome of the avian malaria parasite Haemoproteus majoris (lineage WW2) and its relationship to other Plasmodium species." Avian malaria parasites form a highly prevalent and genetically diverse group within the haemosporidians, yet they...
malaria_HaemoproteusWW2_githubarchive.tar.gz
Aug 5, 2026 - Replication Data for: The genome of the avian malaria parasite Haemoproteus majoris (lineage WW2) and its relationship to other Plasmodium species
Gzip Archive - 1.3 MB - MD5: 05f79c3754ecdb187aa28d5caf9cc54f
CodeDocumentation
Compressed archive of the GitHub which provides all the bioinformatic details of the scripts used to generate the genome and its annotation. The original is available here: https://github.com/mikafontaine/malaria_HaemoproteusWW2.
ReadMe_DOI_10_23708_0QPMON.txt
Aug 5, 2026 - Replication Data for: The genome of the avian malaria parasite Haemoproteus majoris (lineage WW2) and its relationship to other Plasmodium species
Plain Text - 2.6 KB - MD5: 8dc0b5a6fe090c38c1feb4183cd0149d
Documentation
contains the citation, description and conditions of use, or even access, depending on the case, to the dataset
WW2.ILRA.fasta.gz
Aug 5, 2026 - Replication Data for: The genome of the avian malaria parasite Haemoproteus majoris (lineage WW2) and its relationship to other Plasmodium species
Gzip Archive - 6.3 MB - MD5: 538f59792015594f54fffeabac1bafd7
Données
Original genome assembly for Haemoproteus majoris (lineage WW2). The genome was assembled using Nanopore long-read sequencing and polished with Illumina short-reads, yielding 145 contigs with a total assembly size of 23.9Mb and a G+C content of 27.85%. More details are provided i...
WW2_hardmaskup.gff3.gz
Aug 5, 2026 - Replication Data for: The genome of the avian malaria parasite Haemoproteus majoris (lineage WW2) and its relationship to other Plasmodium species
Gzip Archive - 749.1 KB - MD5: 3f41fe888c5a06d338be77d8245db71e
Données
Genome annotations associated with the WW2 reference assembly. The genome annotation was generated using the tool Companion (v2.2.11, Release 63) (Haese-Hill W, Crouch K, Otto TD. 2024, https://doi.org/10.1093/nar/gkae378). More details are provided in the manuscript and the asso...
Replication Data and Scripts : ViroSeek a viral detection pipeline for second-generation sequencing
Replication Data and Scripts : ViroSeek a viral detection pipeline for second-generation sequencing
Jul 28, 2026
Berger, Audric; Lefebvre, Margaux; Dainat, Jacques; Jiolle, Davy; Conclois, Isabelle; Talignani, Loic; Mastriani, Emilio; Cornelie, Sylvie; Berthet, Nicolas; Paupy, Christophe, 2026, "Replication Data and Scripts : ViroSeek a viral detection pipeline for second-generation sequencing", https://doi.org/10.23708/LTXIKA, DataSuds, V2, UNF:6:6xWLtYNtB6mlWqJirEWO9w== [fileUNF]
This repository contains all the files needed to reproduce the results of the article "ViroSeek: a viral detection pipeline for second-generation sequencing", including the files needed to run the ViroSeek pipeline. ViroSeek is a simplified bioinformatics pipeline for the taxonom...
ReadMe.txt
Jul 28, 2026 - Replication Data and Scripts : ViroSeek a viral detection pipeline for second-generation sequencing
Plain Text - 3.0 KB - MD5: f7a1adcb8164f01c0df6bdd70a6915e5
Documentation
contains information for understanding the dataset, including a list of each file deposited and its role, in relation to the structure of the files within this repository.
Viralmetagenome.sh
Jul 28, 2026 - Replication Data and Scripts : ViroSeek a viral detection pipeline for second-generation sequencing
Shell Script - 308 B - MD5: 4df3fc615e6542de1cab355a3c856fd2
Code
Viralmetagenome command script.
Viralmetagenome_input.tab
Jul 28, 2026 - Replication Data and Scripts : ViroSeek a viral detection pipeline for second-generation sequencing
Tabular Data - 658 B - 3 Variables, 5 Observations - UNF:6:jTmqDDNM4j3t0aAGiilaCA==
Données
Viralmetagenome samples input file, companion file of Viralmetagenome.sh.
compile2.py
Jul 28, 2026 - Replication Data and Scripts : ViroSeek a viral detection pipeline for second-generation sequencing
Python Source Code - 3.7 KB - MD5: d35404f2eff0237f1839c10fdfeac401
Code
Script for summarising for each taxonomic assignment
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