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-# RQC: Reads Quality Control #
-
-
- | Catalina (10.15.7) | Big Sure (11.6.3) | Monterey (12.6.0) | Ventura (13.0.1)/E6055C?icon=apple&label&list=|&scale=0.9>)
- | Focal Fossa (20.04) | Jammy Jellyfish (22.04)/772953?icon=https://www.svgrepo.com/show/25424/ubuntu-logo.svg&label&list=|&scale=0.9>)
- | Focal Fossa (20.04) | Jammy Jellyfish (22.04)/00BCF2?icon=windows&label&list=|&scale=0.9>)
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-## ~ ABOUT ~ ##
-
-
-### RQC ###
-
-RQC is a FAIR, open-source, scalable, modulable and traceable snakemake pipeline, used for Illumina Inc. short reads quality controls.
-RQC is included as first step of **[GeVarLi](https://www.afroscreen.org/)** workflow.
-
-
-### Genomic sequencing, a public health tool ###
-
-The establishment of a surveillance and sequencing network is an essential public health tool for detecting and containing pathogens with epidemic potential. Genomic sequencing mak\
-es it possible to identify pathogens, monitor the emergence and impact of variants, and adapt public health policies accordingly.
-
-The Covid-19 epidemic has highlighted the disparities that remain between continents in terms of surveillance and sequencing systems. At the end of October 2021, of the 4,600,000 s\
-equences shared on the public and free GISAID tool worldwide, only 49,000 came from the African continent, i.e. less than 1% of the cases of Covid-19 diagnosed on this continent.
-
-### Features ###
-
-- Reads quality control
- - Fastq-Screen
- - FastQC
- - MultiQC (_html report_)
-
-
-### Version ###
-
-*V.2022.11*
-
-
-### Rulegraph ###
-
-<img src="./resources/visuals/quality_control_rulegraph.png" width="250" height="150">
-
-
-## ~ SUPPORT ~ ##
-
-1. Read The Fabulous Manual!
-2. Read de Awsome Wiki!
-3. Create a new issue: Issues > New issue > Describe your issue
-4. Send an email to [nicolas.fernandez@ird.fr](url)
-
-## ~ CITATION ~ ##
-
-If you use this pipeline, *please* cite this *RQC*, GitLab IRDForge repository and authors:
-
-GitLab IRDForge repository: [https://forge.ird.fr/transvihmi/nfernandez/RQC](https://forge.ird.fr/transvihmi/nfernandez/RQC)
-
-RQC, a FAIR, open-source, scalable, modulable and traceable snakemake pipeline,
-for Illumina Inc. short reads quality controls.
-
-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)_
-
-
-## ~ AUTHORS & ACKNOWLEDGMENTS ~ ##
-
-- Nicolas Fernandez - IRD _(Developer and Maintener)_
-- Christelle Butel - IRD _(Reporter)_
-- DALL•E mini - OpenAI [Git](https://github.com/borisdayma/dalle-mini) _(Repo. avatar)_
-
-
-## ~ LICENSE ~ ##
-
-Licencied under [GPLv3](https://www.gnu.org/licenses/gpl-3.0.html)
-Intellectual property belongs to [IRD](https://www.ird.fr/) and authors.
-
-
-## ~ ROADMAP ~ ##
-
-- Add MultiQC config template
-
-
-## ~ PROJECT STATUS ~ ##
-
-This project is **regularly update** and **actively maintened**
-However, you can be volunteer to step in as **developer** or **maintainer**
-
-
-## ~ CONTRIBUTING ~ ##
-
-Open to contributions!
-
-- Asking for update
-- Proposing new feature
-- Reporting issue
-- Fixing issue
-- Sharing code
-- Citing tool
-
-
-## ~ INSTALLATIONS ~ ##
-
-# Conda _(dependencies)_ #
-
-RQC use the usefull **Conda** environment manager
-So, if and only if, it's required _(Conda not already installed)_, please, first install **Conda**!
-
-Download and install your OS adapted version of [Latest Miniconda Installer](https://docs.conda.io/en/latest/miniconda.html#latest-miniconda-installer-links)
-
-e.g. for **MacOSX-64-bit** systems:
-```shell
-curl https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh -o ~/Miniconda3-latest-MacOSX-x86_64.sh && \
-bash ~/Miniconda3-latest-MacOSX-x86_64.sh -b -p ~/miniconda3/ && \
-rm -f ~/Miniconda3-latest-MacOSX-x86_64.sh && \
-~/miniconda3/condabin/conda update conda --yes && \
-~/miniconda3/condabin/conda init && \
-exit
-```
-
-e.g. for **Linux-64-bit** systems:
-```shell
-curl https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -o ~/Miniconda3-latest-Linux-x86_64.sh && \
-bash ~/Miniconda3-latest-Linux-x86_64.sh -b -p ~/miniconda3/ && \
-rm -f ~/Miniconda3-latest-Linux-x86_64.sh && \
-~/miniconda3/condabin/conda update conda --yes && \
-~/miniconda3/condabin/conda init && \
-exit
-```
-
-Update Conda:
-```
-conda update -n base -c defaults conda
-```
-
-
-# RQC #
-
-Clone to your home/ [RQC](https://forge.ird.fr/transvihmi/nfernandez/Reads_Quality_Control) GitLab IRDForg repository _(ID: 404)_:
-```shell
-git https://forge.ird.fr/transvihmi/nfernandez/RQC.git ~/RQC/
-```
-
-Update RQC:
-
-```shell
-cd ~/RQC/ && git reset --hard HEAD && git pull --verbose
-```
-
-## ~ USAGE ~ ##
-
-1. Copy your **reads** _(single or paired-ends)_ in **.fastq.gz** or **fastq** formats files into: **./resources/reads/** directory
-
-2. Execute **Start_RQC.sh** bash script to run GeVarLi pipeline _(according to your choice)_:
- - or with a **Double-click** on it _(if you make .sh files executable files with Terminal.app)_
- - or with a **Right-click** > **Open with** > **Terminal.app**
- - or with **CLI** from a terminal:
-```shell
-bash Start_RQC.sh
-```
-3. Yours analyzes will start, with default configuration settings
-
-_Option-1: Edit **config.yaml** file in **./config/** directory_
-_Option-2: Edit **fastq-screen.conf** file in **./config/** directory_
-
-First run will auto-created _(only once)_:
- - Snakemake-Base conda environment _(Snakemake, Mamba, Rename, GraphViz)_
- - RQC-conda environments _(for each tools used by RQC)_
- - Indexes for BWA aligner _(for each fasta genomes in resources)_
-
-_This may take some time, depending on your internet connection and your computer_
-
-
-## ~ RESULTS ~ ##
-
-Yours results are available in **./results/** directory, as follow:
-
-```shell
- 🧩 Reads_Quality_Control/
- └── 📂 results/
- ├── 🌠All_readsQC_reports.html
- ├── 📂 00_Quality_Control/
- │ ├── 📂 fastq-screen/
- │ │ ├── 🌠{SAMPLE}_R{1/2}_screen.html
- │ │ ├── 📈 {SAMPLE}_R{1/2}_screen.png
- │ │ └── 📄 {SAMPLE}_R{1/2}_screen.txt
- │ ├── 📂 fastqc/
- │ │ ├── 🌠{SAMPLE}_R{1/2}_fastqc.html
- │ │ └── 📦 {SAMPLE}_R{1/2}_fastqc.zip
- │ └── 📂 multiqc/
- │   ├── 🌠multiqc_report.html
- │ └──📂 multiqc_data/
- │    ├── 📠multiqc.log
- │    ├── 📄 multiqc_citations.txt
- │    ├── 🌀 multiqc_data.json
- │    ├── 📄 multiqc_fastq_screen.txt
- │    ├── 📄 multiqc_fastqc.txt
- │    ├── 📄 multiqc_general_stats.txt
- |    └── 📄 multiqc_sources.txt
- └── 📂 10_Reports/
-  ├── âš™ï¸ config.log
-  ├── 📠settings.log
-  ├── 🜠RQC-Base_v.{VERSION}.yaml
- ├── 📂 files-summaries
-  │ └── 📄 Reads_Quality_Control_files-summary.txt
-  ├── 📂 graphs/
-  │ ├── 📈 Reads_Quality_Control_dag.{PNG/PDF}
-  │ ├── 📈 Reads_Quality_Control_filegraph.{PNG/PDF}
-  │ └── 📈 Reads_Quality_Control_rulegraph.{PNG/PDF}
-  └── 📂 tools-log/
- ├── 📂 bowtie2/
- ├── 📂 bwa/
- ├── 📠fastq-screen.log
- ├── 📠fastqc.log
-   └── 📠multiqc.log
-```
-
-### fastq-screen ###
-
-Search in your libraries if the genomes of organisms you work on, along with PhiX, Vectors,
-or other contaminants commonly seen in sequencing experiments.
-More about [fastq-screen](https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/)
-
-
-### fastqc ###
-
-Modular set of analyses which you can use to give a quick impression of whether
-your data has any problems of which you should be aware before doing any further analysis.
-More about [fastqc](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
-
-
-### multiqc ###
-
-Compiled HTML report. More about [multiqc](https://multiqc.info/)
-
-
-## ~ CONFIGURATION ~ ##
-
-You can edit default settings in **config.yaml** file into **./config/** directory:
-
-### Resources ###
-
-Edit to match your hardware configuration
-- **cpus**: for tools that can _(i.e. bwa)_, could be use at most n cpus to run in parallel _(default config: '8')_
-_**Note**: snakemake (with default Start bash script) will always use all cpus to parallelize jobs_
-- **ram**: for tools that can _(i.e. samtools)_, limit memory usage to max n Gb _(default config: '16' Gb)_
-- **tmpdir**: for tools that can _(i.e. pangolin)_, specify where you want the temp stuff _(default config: '$TMPDIR')_
-
-
-### Environments ###
-
-Edit if you want change some environments _(e.g. test a new version)_ in ./workflow/envs/{tools}_v.{version}.yaml files
-
-
-### Fastq-Screen ###
-
-- **config**: path to the fastq-screen configuration file _(default config: ./config/fastq-screen.conf)_
-- **subset**: do not use the whole sequence file, but create a temporary dataset of this specified number of read _(default config: '1000')_
-- **aligner**: specify the aligner to use for the mapping. Valid arguments are 'bowtie', bowtie2' or 'bwa' _(default config: 'bwa')_
-
-#### fastq-screen.conf ####
-
-- **databases**: enables you to configure multiple genomes databases _(aligner index files)_ to search against
-
-
-### RQC map ###
-
-```shell
- 🧩 Reads_Quality_Control/
- ├── ðŸ–¥ï¸ Start_GeVarLi.sh
- ├── 📚 README.md
- ├── 🪪 LICENSE
- ├── 🛑 .gitignore
- ├── 📂 .git/
- ├── 📂 .snakemake/
- ├── 📂 config/
- │ ├── âš™ï¸ config.yaml
- │ └── âš™ï¸ fastq-screen.conf
- ├── 📂 resources/
- │ ├── 📂 genomes/
- │ │ ├── 🧬 SARS-CoV-2_Wuhan_MN908947-3.fasta
- │ │ ├── 🧬 Monkeypox-virus_Zaire_AF380138-1.fasta
- │ │ ├── 🧬 Monkeypox-virus_UK_MT903345-1.fasta
- │ │ ├── 🧬 Swinepox-virus_India_MW036632-1.fasta
- │ │ ├── 🧬 Ebola-virus_Zaire_AF272001-1.fasta
- │ │ ├── 🧬 Nipah-virus_Malaysia_AJ564622-1.fasta
- │ │ ├── 🧬 HIV-1_HXB2_K03455-1.fasta.fasta
- │ │ ├── 🧬 (your_favorite_genome_reference}.fasta
- │ │ ├── 🧬 QC_Echerichia-coli_CP060121-1.fasta
- │ │ ├── 🧬 QC_Kanamycin-Resistance-Gene.fasta
- │ │ ├── 🧬 QC_NGS-adapters.fasta
- │ │ ├── 🧬 QC_phi-X174_Coliphage_NC-001422-1.fasta
- │ │ ├── 🧬 QC_UniVec_wo_phiX_and_kanamycin.fasta
- │ │ └── 🧬 {your_favorite_qc_reference}.fasta
- │ ├── 📂 indexes/
- │ │ └── 📂 bwa/
- │ │ ├── ðŸ—‚ï¸ {GENOME}.amb
- │ │ ├── ðŸ—‚ï¸ {GENOME}.ann
- │ │ ├── ðŸ—‚ï¸ {GENOME}.bwt
- │ │ ├── ðŸ—‚ï¸ {GENOME}.pac
- │ │ └── ðŸ—‚ï¸ {GENOME}.sa
- │ ├── 📂 reads/
- │ │ ├── ðŸ›¡ï¸ .gitkeep
- │ │ ├── 📦 {SAMPLE}_R1.fastq.gz
- │ │ └── 📦 {SAMPLE}_R2.fastq.gz
- │ └── 📂 visuals/
- │ └── 📈 quality_control_rulegraph.png
- └── 📂 workflow/
- ├── 📂 envs/
- │ ├── 📂 linux/
- │ │ ├── 🜠bwa_v.0.7.17.yaml
- │ │ ├── 🜠fastq-screen_v.0.15.2.yaml
- │ │ ├── 🜠fastqc_v.0.11.9.yaml
- │ │ ├── 🜠multiqc_v.1.12.yaml
- │ │ └── 🜠snakemake-base_v.2023.02.yaml
- │ └── 📂 osx/
- │ ├── 🜠bwa_v.0.7.17.yaml
- │ ├── 🜠fastq-screen_v.0.15.2.yaml
- │ ├── 🜠fastqc_v.0.11.9.yaml
- │ ├── 🜠multiqc_v.1.12.yaml
- │ └── 🜠snakemake-base_v.2023.02.yaml
- └── 📂 rules/
- ├── 📜 indexing_genomes.smk
- └── 📜 quality_control.smk
-```
-
-
-## ~ REFERENCES ~ ##
-
-**Sustainable data analysis with Snakemake**
-Felix Mölder, Kim Philipp Jablonski, Brice Letcher, Michael B. Hall, Christopher H. Tomkins-Tinch, Vanessa Sochat, Jan Forster, Soohyun Lee, Sven O. Twardziok, Alexander Kanitz, Andreas Wilm, Manuel Holtgrewe, Sven Rahmann, Sven Nahnsen, Johannes Köster
-_F1000Research (2021)_
-**DOI**: [https://doi.org/10.12688/f1000research.29032.2](https://doi.org/10.12688/f1000research.29032.2)
-**Publication**: [https://f1000research.com/articles/10-33/v1](https://f1000research.com/articles/10-33/v1)
-**Source code**: [https://github.com/snakemake/snakemake](https://github.com/snakemake/snakemake)
-**Documentation**: [https://snakemake.readthedocs.io/en/stable/index.html](https://snakemake.readthedocs.io/en/stable/index.html)
-
-**Anaconda Software Distribution**
-Team
-_Computer software (2016)_
-**DOI**: []()
-**Publication**: [https://www.anaconda.com](https://www.anaconda.com)
-**Source code**: [https://github.com/snakemake/snakemake](https://github.com/snakemake/snakemake) (conda)
-**Documentation**: [https://snakemake.readthedocs.io/en/stable/index.html](https://snakemake.readthedocs.io/en/stable/index.html) (conda)
-**Source code**: [https://github.com/mamba-org/mamba](https://github.com/mamba-org/mamba) (mamba)
-**Documentation**: [https://mamba.readthedocs.io/en/latest/index.html](https://mamba.readthedocs.io/en/latest/index.html) (mamba)
-
-**Fast and accurate short read alignment with Burrows-Wheeler Transform**
-Heng Li and Richard Durbin
-_Bioinformatics, Volume 25, Aricle 1754-60 (2009)_
-**DOI**: [https://doi.org/10.1093/bioinformatics/btp324](https://doi.org/10.1093/bioinformatics/btp324)
-**Publication**: [https://pubmed.ncbi.nlm.nih.gov/19451168@](https://pubmed.ncbi.nlm.nih.gov/19451168)
-**Source code**: [https://github.com/lh3/bwa](https://github.com/lh3/bwa)
-**Documentation**: [http://bio-bwa.sourceforge.net](http://bio-bwa.sourceforge.net)
-
-**MultiQC: summarize analysis results for multiple tools and samples in a single report**
-Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
-_Bioinformatics, Volume 32, Issue 19 (2016)_
-**DOI**: [https://doi.org/10.1093/bioinformatics/btw354](https://doi.org/10.1093/bioinformatics/btw354)
-**Publication**: [https://academic.oup.com/bioinformatics/article/32/19/3047/2196507](https://academic.oup.com/bioinformatics/article/32/19/3047/2196507)
-**Source code**: [https://github.com/ewels/MultiQC](https://github.com/ewels/MultiQC)
-**Documentation**: [https://multiqc.info](https://multiqc.info)
-
-**FastQ Screen: A tool for multi-genome mapping and quality control**
-Wingett SW and Andrews S
-_F1000Research (2018)_
-**DOI**: [https://doi.org/10.12688/f1000research.15931.2](https://doi.org/10.12688/f1000research.15931.2)
-**Publication**: [https://f1000research.com/articles/7-1338/v2](https://f1000research.com/articles/7-1338/v2)
-**Source code**: [https://github.com/StevenWingett/FastQ-Screen](https://github.com/StevenWingett/FastQ-Screen)
-**Documentation**: [https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen](https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen)
-
-**FastQC: A quality control tool for high throughput sequence data**
-Simon Andrews
-_Online (2010)_
-**DOI**: [https://doi.org/](https://doi.org/)
-**Publication**: []()
-**Source code**: [https://github.com/s-andrews/FastQC](https://github.com/s-andrews/FastQC)
-**Documentation**: [https://www.bioinformatics.babraham.ac.uk/projects/fastqc](https://www.bioinformatics.babraham.ac.uk/projects/fastqc)
-
-
-###############################################################################
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