UMR MIVEGEC

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.

Porpoises genetics and genomics

REACT Project

REACT2 Project

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51 to 60 of 269 Results

Taxprofiler.sh Mar 4, 2026 - Replication Data and Scripts : ViroSeek a viral detection pipeline for second-generation sequencing Shell Script - 532 B - MD5: 0b1dba73a89694a8786f937eeffec0e4 Code Taxprofiler command script.
taxprof_ressouces.config Mar 4, 2026 - Replication Data and Scripts : ViroSeek a viral detection pipeline for second-generation sequencing Unknown - 103 B - MD5: 653be8d086a3fe012cc314f1778222d6 Code Configuration file for Taxprofiler execution, companion file of Taxprofiler.sh.
trimgalore.nf Mar 4, 2026 - Replication Data and Scripts : ViroSeek a viral detection pipeline for second-generation sequencing Nextflow Script - 608 B - MD5: b85ebab75a77b0fa51ff011d4e8daf9b Code Modules for ViroSeek
Viroseek_downstream_analysis.Rmd Mar 4, 2026 - Replication Data and Scripts : ViroSeek a viral detection pipeline for second-generation sequencing R Notebook - 26.7 KB - MD5: 5388991cf49f2d17c247556d77e1860e Code Rmarkdown for downstream analysis
ViroSeek_input.tab Mar 4, 2026 - Replication Data and Scripts : ViroSeek a viral detection pipeline for second-generation sequencing Tabular Data - 733 B - 3 Variables, 5 Observations - UNF:6:tyuLW2kmYZtk+8pIMV/RPQ== Données ViroSeek samples input file, companion file of Viroseek.sh.
ViroSeek_installation.txt Mar 4, 2026 - Replication Data and Scripts : ViroSeek a viral detection pipeline for second-generation sequencing Plain Text - 4.1 KB - MD5: a1d94219484866a57a948d13881802b9 Documentation Installation instructions for ViroSeek.
ViroSeek.nf Mar 4, 2026 - Replication Data and Scripts : ViroSeek a viral detection pipeline for second-generation sequencing Nextflow Script - 14.9 KB - MD5: d6ab166a9087903150a31e61072a1e08 Code Nextflow pipeline script for ViroSeek.
Viroseek.sh Mar 4, 2026 - Replication Data and Scripts : ViroSeek a viral detection pipeline for second-generation sequencing Shell Script - 537 B - MD5: 5f26695e80c215ec06a2d729eb968035 Code ViroSeek command script, used in this study.
ViroSeek_use.txt Mar 4, 2026 - Replication Data and Scripts : ViroSeek a viral detection pipeline for second-generation sequencing Plain Text - 3.7 KB - MD5: a227c3711141ee2641eacea0422e3066 Documentation Tutorial for running ViroSeek pipeline.
virus_genome_to_id.tab Mar 4, 2026 - Replication Data and Scripts : ViroSeek a viral detection pipeline for second-generation sequencing Tabular Data - 202 B - 2 Variables, 3 Observations - UNF:6:u5bQZ+jVWrdnqQ55z0s0Ug== Données Companion file for CAMISIM_script.sh (tsv version)

Taxprofiler.sh

Mar 4, 2026 - Replication Data and Scripts : ViroSeek a viral detection pipeline for second-generation sequencing

Shell Script - 532 B -

Code

Taxprofiler command script.

taxprof_ressouces.config

Mar 4, 2026 - Replication Data and Scripts : ViroSeek a viral detection pipeline for second-generation sequencing

Unknown - 103 B -

Code

Configuration file for Taxprofiler execution, companion file of Taxprofiler.sh.

trimgalore.nf

Mar 4, 2026 - Replication Data and Scripts : ViroSeek a viral detection pipeline for second-generation sequencing

Nextflow Script - 608 B -

Code

Modules for ViroSeek

Viroseek_downstream_analysis.Rmd

Mar 4, 2026 - Replication Data and Scripts : ViroSeek a viral detection pipeline for second-generation sequencing

R Notebook - 26.7 KB -

Code

Rmarkdown for downstream analysis

ViroSeek_input.tab

Mar 4, 2026 - Replication Data and Scripts : ViroSeek a viral detection pipeline for second-generation sequencing

Tabular Data - 733 B - 3 Variables, 5 Observations -

Données

ViroSeek samples input file, companion file of Viroseek.sh.

ViroSeek_installation.txt

Mar 4, 2026 - Replication Data and Scripts : ViroSeek a viral detection pipeline for second-generation sequencing

Plain Text - 4.1 KB -

Documentation

Installation instructions for ViroSeek.

ViroSeek.nf

Mar 4, 2026 - Replication Data and Scripts : ViroSeek a viral detection pipeline for second-generation sequencing

Nextflow Script - 14.9 KB -

Code

Nextflow pipeline script for ViroSeek.

Viroseek.sh

Mar 4, 2026 - Replication Data and Scripts : ViroSeek a viral detection pipeline for second-generation sequencing

Shell Script - 537 B -

Code

ViroSeek command script, used in this study.

ViroSeek_use.txt

Mar 4, 2026 - Replication Data and Scripts : ViroSeek a viral detection pipeline for second-generation sequencing

Plain Text - 3.7 KB -

Documentation

Tutorial for running ViroSeek pipeline.

virus_genome_to_id.tab

Mar 4, 2026 - Replication Data and Scripts : ViroSeek a viral detection pipeline for second-generation sequencing

Tabular Data - 202 B - 2 Variables, 3 Observations -

Données

Companion file for CAMISIM_script.sh (tsv version)

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