RQCP: Reads Quality Control Pipeline
Description
RQCP check NGS (illumina) reads quality and clean it if needed, as you set, using:
- Cutadapts to trim NGS sequencing adapters
- Sickle-trim to trim reads on base-calling quality score
- Fastq-join to join mates reads (forward R1 and Reverse R2) when it's possible
- FastQC to check global quality
- FastqScreen to check putative contamination(s)
- MultiQC to generate HTML reports
Badges
Visuals
Good idea to include screenshots or GIFs (see ttygif or Asciinema)
Installation
Command-Line
Clone with SSH when you want to authenticate only one time
Authenticate with GitLab by following the instructions in the SSH documentation
git clone git@gitlab.com:ird_transvihmi/Reads_Quality_Control_Pipeline.git
Clone with HTTPS when you want to authenticate each time you perform an operation between your computer and GitLab
git clone https://gitlab.com/ird_transvihmi/Reads_Quality_Control_Pipeline.git
Web-Interface
Download reads_quality_control project directory
Difference between download and clone
To create a copy of a remote repository’s files on your computer, you can either download or clone the repository
If you download it, you cannot sync the repository with the remote repository on GitLab
Cloning a repository is the same as downloading, except it preserves the Git connection with the remote repository
You can then modify the files locally and upload the changes to the remote repository on GitLab
Usage
Make sure your bash script is executable
Edit config.yaml file on config directory (option)
Edit fastq-screen config file on config directory (option)
Run RQC.sh bash script by double-clicking on it
manual
to do quick !
Support
- RTFM! (Read The Fabulous Manual! ^^.)
- Read de awsome wiki ;)
- Create a new issue: Issues > New issue > Describe your issue
- Send an email to nicolas.fernandez@ird.fr
- Call me to
+33.(0)4.67.41.55.°°; No, don't please ! O_o
Roadmap
Add new features
Contributing
Open to contributions :)
Testing code, finding issues, asking for update, proposing new features ...
Use Git tools to share !
Authors and acknowledgment
- Nicolas Fernandez (Maintener)
- Christelle Butel for testing all versions of this script
License
Project status
I'm out of time for this project, development has slowed down, close to stopped completely
You can be volunteer to step in as a maintainer ;)
Or choose to fork this project allowing this project to keep going !
For information :
- Guests are not active contributors in private projects, they can only see, and leave comments and issues.
- Reporters are read-only contributors, they can't write to the repository, but can on issues.
- Developers are direct contributors, they have access to everything to go from idea to production, unless something has been explicitly restricted.
- Maintainers are super-developers, they are able to push to master, deploy to production. This role is often held by maintainers and engineering managers.
- Owners are essentially group-admins, they can give access to groups and have destructive capabilities.
Project status
If you have run out of energy or time for your project, put a note at the top of the README saying that development has slowed down or stopped completely. Someone may choose to fork your project or volunteer to step in as a maintainer or owner, allowing your project to keep going. You can also make an explicit request for maintainers.