GeVarLi: GEnome Assembly, VARiant calling and LIneage assignation

GeVarLi is a FAIR, open-source, scalable, modulable and traceable snakemake pipeline, used for SARS-CoV-2 (and others viruses) genome assembly and 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).

About

GeVarLi is a FAIR, open-source, scalable, modulable and traceable snakemake pipeline, used for SARS-CoV-2 (and others viruses) genome assembly and 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

• Documentations: Read The Fabulous Manual
• Raise issues and report bugs: https://forge.ird.fr!
• Contact: nicolas.fernandez@ird.fr

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