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Author MacOSX - Intel x86-64 / ARM Apple Silicon GNU-Linux - Ubuntu / WSL Issues closed Issues opened Maintened Webpage Open Source GNU AGPL v3 Gitlab Bash Python Snakemake Conda

GeVarLi: Genome assembly, Variant calling and Lineage assignation

About

GeVarLi is a FAIR, open-source, scalable, modulable and traceable snakemake pipeline, used for SARS-CoV-2, and others viruses, genome assembly, variants monitoring, using Illumina Inc. short reads COVIDSeq™ libraries sequencing.

GeVarLi was initialy developed in intern (Oct. 2021) for AFROSCREEN project, before public release on GitLab (Mar. 2022).

Support

Citation

GeVarLi, a FAIR, open-source, scalable, modulable and traceable snakemake pipeline, for reference-based Genome assembly and Variants calling and Lineage assignment, from SARS-CoV-2 to others (re)emergent viruses, Illumina short reads sequencing.

GitLab IRDForge repository: https://forge.ird.fr/transvihmi/nfernandez/GeVarLi

Nicolas FERNANDEZ NUÑEZ (1), Eddy KINGADA LUSAMAKI (1, 2, 3), Thibaut Armel CHÉRIF GNIMADI (4), Nicole VIDALE (1), Christelle BUTEL (1), Laeticia SERRANO (1), Célestin GODWE (5, 6), Martine PEETERS (1) and Ahidjo AYOUBA (1)

(1) UMI 233 - Recherches Translationnelles sur le VIH et les Maladies Infectieuses endémiques et émergentes (TransVIHMI), University of Montpellier (UM), French National Research Institute for Sustainable Development (IRD), French Institute of Health and Medical Research (INSERM), Moontpellier, France

(2) Institut National de Recherche Biomédicale (INRB), Kinshasa, Democratic Republic of the Congo

(3) Service de Microbiologie, Département de Biologie Médicale, Cliniques Universitaires de Kinshasa, Université de Kinshasa, Kinshasa, Democratic Republic of the Congo

(4) Centre de Recherche et de Formation en Infectiologie de Guinée (CERFIG), Université Gamal Abder Nasser de Conakry, Conakry, Guinea

(5) Center of Research for Emerging and Re-Emerging Diseases (CREMER), Institute of Medical Research and Study of Medicinal Plants (IMPM), Yaoundé, Cameroon

(6) Department of Biochemistry, University of Douala, Douala, Cameroon