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Doc: update index (en)

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README.md
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![Snakemake](<https://badgen.net/badge/icon/Snakemake 8.25.3/black?icon=https://upload.wikimedia.org/wikipedia/commons/d/d3/Python_icon_%28black_and_white%29.svg&label&scale=0.9>)
![Conda](<https://badgen.net/badge/icon/Conda 24.11.0/black?icon=codacy&label&scale=0.9>)
# 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&trade; libraries sequencing.
GeVarLi was initialy developed in intern (Oct. 2021) for **[AFROSCREEN](https://www.afroscreen.org/)** project, before public release on GitLab (Mar. 2022).
# GeVarLi: **Ge**nome assembly, **Var**iant calling and **Li**neage assignation
## 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&trade; libraries sequencing.
**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&trade; libraries sequencing.
GeVarLi was initialy developed in intern (Oct. 2021) for **[AFROSCREEN](https://www.afroscreen.org/)** project, before public release on GitLab (Mar. 2022).
**GeVarLi** was initialy developed in intern (Oct. 2021) for **[AFROSCREEN](https://www.afroscreen.org/)** project, before public release on GitLab (Mar. 2022).
## Support
......@@ -37,11 +31,22 @@ GeVarLi was initialy developed in intern (Oct. 2021) for **[AFROSCREEN](https://
## Citation
GeVarLi, a FAIR, open-source, scalable, modulable and traceable snakemake pipeline,
**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.
from SARS-CoV-2 to others (re)emergent viruses, Illumina short reads sequencing.**
GitLab IRDForge repository: [https://forge.ird.fr/transvihmi/nfernandez/GeVarLi](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)_
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_
documentations/en/index.md
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![Snakemake](<https://badgen.net/badge/icon/Snakemake 8.25.3/black?icon=https://upload.wikimedia.org/wikipedia/commons/d/d3/Python_icon_%28black_and_white%29.svg&label&scale=0.9>)
![Conda](<https://badgen.net/badge/icon/Conda 24.11.0/black?icon=codacy&label&scale=0.9>)
# 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&trade; libraries sequencing.
GeVarLi was initialy developed in intern (Oct. 2021) for **[AFROSCREEN](https://www.afroscreen.org/)** project, before public release on GitLab (Mar. 2022).
# GeVarLi: **Ge**nome assembly, **Var**iant calling and **Li**neage assignation
## 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&trade; libraries sequencing.
**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&trade; libraries sequencing.
GeVarLi was initialy developed in intern (Oct. 2021) for **[AFROSCREEN](https://www.afroscreen.org/)** project, before public release on GitLab (Mar. 2022).
**GeVarLi** was initialy developed in intern (Oct. 2021) for **[AFROSCREEN](https://www.afroscreen.org/)** project, before public release on GitLab (Mar. 2022).
## Support
......@@ -36,11 +31,22 @@ GeVarLi was initialy developed in intern (Oct. 2021) for **[AFROSCREEN](https://
## Citation
GeVarLi, a FAIR, open-source, scalable, modulable and traceable snakemake pipeline,
**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.
from SARS-CoV-2 to others (re)emergent viruses, Illumina short reads sequencing.**
GitLab IRDForge repository: [https://forge.ird.fr/transvihmi/nfernandez/GeVarLi](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)_
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_
documentations/en/pages/features.md
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# Fonctionnalités et outils
# Features and tools
## Gestionnaire de pipeline
- Workflow ................................. Snakemake
- Environnements ........................... Miniforge _(Conda)_
## Workflow management
- Workflow ......................... Snakemake
- Environments ..................... Miniforge _(Conda)_
## Qualité contrôle des lectures
- Contrôle des contaminations .............. Fastq-Screen
- Mesures qualités des lectures ............ FastQC
- Rapport qualité HTML ..................... MultiQC
## Reads quality control
- Contamination checking ........... Fastq-Screen
- Reads qualities metrics .......... FastQC
- HTML reporting ................... MultiQC
## Nettoyage des lectures
- Nettoyage des adaptateurs Illumina ....... Cutadapt
- Nettoyage des primers d'amplicons ........ Cutadapt _('hard-clipping')_
- Nettoyage des lectures basses qualités ... Sickle-trim
## Reads cleaning
- Illumina adpters trimming ........ Cutadapt
- Amplicon primers trimming ........ Cutadapt _('hard-clipping')_
- Reads quality trimming ........... Sickle-trim
## Allignement des lectures
- Indexation des genomes ................... BWA _(ou minimap2, ou bowtie2)_
- Allignement des lectures ................. BWA _(ou minimap2, ou bowtie2)_
- Nettoyage des primers d'amplicons ........ Bamclipper _('soft-clipping')_
- Visualisation _(avec IGV)_ ................. fichiers BAM, BAI et BED
- Rapport de couverture génomique .......... Bedtools _(tableur)_
## Reads mapping
- Indexing genomes ................. BWA _(or minimap2, or bowtie2)_
- Reads mapping .................... BWA _(or minimap2, or bowtie2)_
- Amplicon primers trimming ........ Bamclipper _('soft-clipping')_
- Visualization _(with IGV)_ ......... BAM, BAI and BED files
- Genome coverage reports .......... Bedtools _(table file)_
## Appel de variants
- Filtrage des variants ..................... Ivar
- Appel de variants ......................... Ivar
## Variants calling
- Variants filtering ............... Ivar
- Variants calling ................. Ivar
## Sequences consensus
- Appel du consensus ........................ Ivar _(fichier FASTA)_
## Consensus sequences
- Consensus calling ................ Ivar _(FASTA file)_
## Classification génomiques
- Qualité des génomes SARS-CoV-2 ............ Nextclade
- Assignation lignées Nextclade ............. Nextclade
- Assignation lignées Pangolin .............. Nextclade _(ou Pangolin)_
## Genomes classification
- SARS-CoV-2 genome quality ........ Nextclade
- Nextclade lineages assignation ... Nextclade
- Pangolin lineages assignation .... Nextclade _(or Pangolin)_
## Rulegraph
<img src="../../../images/gevarli_rulegraph.png" width="1200" height="2400">
......
documentations/fr/pages/features.md
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# Features and tools
# Fonctionnalités et outils
## Workflow management
- Workflow ......................... Snakemake
- Environments ..................... Miniforge _(Conda)_
## Gestionnaire de pipeline
- Workflow ................................. Snakemake
- Environnements ........................... Miniforge _(Conda)_
## Reads quality control
- Contamination checking ........... Fastq-Screen
- Reads qualities metrics .......... FastQC
- HTML reporting ................... MultiQC
## Qualité contrôle des lectures
- Contrôle des contaminations .............. Fastq-Screen
- Mesures qualités des lectures ............ FastQC
- Rapport qualité HTML ..................... MultiQC
## Reads cleaning
- Illumina adpters trimming ........ Cutadapt
- Amplicon primers trimming ........ Cutadapt _('hard-clipping')_
- Reads quality trimming ........... Sickle-trim
## Nettoyage des lectures
- Nettoyage des adaptateurs Illumina ....... Cutadapt
- Nettoyage des primers d'amplicons ........ Cutadapt _('hard-clipping')_
- Nettoyage des lectures basses qualités ... Sickle-trim
## Reads mapping
- Indexing genomes ................. BWA _(or minimap2, or bowtie2)_
- Reads mapping .................... BWA _(or minimap2, or bowtie2)_
- Amplicon primers trimming ........ Bamclipper _('soft-clipping')_
- Visualization _(with IGV)_ ......... BAM, BAI and BED files
- Genome coverage reports .......... Bedtools _(table file)_
## Allignement des lectures
- Indexation des genomes ................... BWA _(ou minimap2, ou bowtie2)_
- Allignement des lectures ................. BWA _(ou minimap2, ou bowtie2)_
- Nettoyage des primers d'amplicons ........ Bamclipper _('soft-clipping')_
- Visualisation _(avec IGV)_ ................. fichiers BAM, BAI et BED
- Rapport de couverture génomique .......... Bedtools _(tableur)_
## Variants calling
- Variants filtering ............... Ivar
- Variants calling ................. Ivar
## Appel de variants
- Filtrage des variants ..................... Ivar
- Appel de variants ......................... Ivar
## Consensus sequences
- Consensus calling ................ Ivar _(FASTA file)_
## Sequences consensus
- Appel du consensus ........................ Ivar _(fichier FASTA)_
## Genomes classification
- SARS-CoV-2 genome quality ........ Nextclade
- Nextclade lineages assignation ... Nextclade
- Pangolin lineages assignation .... Nextclade _(or Pangolin)_
## Classification génomiques
- Qualité des génomes SARS-CoV-2 ............ Nextclade
- Assignation lignées Nextclade ............. Nextclade
- Assignation lignées Pangolin .............. Nextclade _(ou Pangolin)_
## Rulegraph
<img src="../../../images/gevarli_rulegraph.png" width="1200" height="2400">
......
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