Ecosyste.ms: Awesome
An open API service indexing awesome lists of open source software.
https://github.com/labsquare/fastqt
FastQC port to Qt5: A quality control tool for high throughput sequence data.
https://github.com/labsquare/fastqt
bioinformatics fastq fastq-format gui qt5
Last synced: 10 days ago
JSON representation
FastQC port to Qt5: A quality control tool for high throughput sequence data.
- Host: GitHub
- URL: https://github.com/labsquare/fastqt
- Owner: labsquare
- License: gpl-3.0
- Created: 2016-10-27T14:43:37.000Z (about 8 years ago)
- Default Branch: devel
- Last Pushed: 2020-08-04T12:52:43.000Z (over 4 years ago)
- Last Synced: 2024-05-01T21:19:21.711Z (8 months ago)
- Topics: bioinformatics, fastq, fastq-format, gui, qt5
- Language: C++
- Homepage:
- Size: 9.17 MB
- Stars: 109
- Watchers: 22
- Forks: 25
- Open Issues: 33
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG
- License: LICENSE
Awesome Lists containing this project
README
# FastQt
 [](https://gitter.im/labsquare/fastQt?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge) [](https://ci.appveyor.com/project/dridk/fastqt) [](https://coveralls.io/github/labsquare/fastQt?branch=master)
FastQt is the clone of [FastQC](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) application ported
from Java to [C++/Qt5](https://www.qt.io/)
## Installation
### Linux
An [AppImage](http://appimage.org/) has been created and should work on recent Linux distribution.
Download the last release from [here](https://github.com/labsquare/fastQt/releases/) and run it as follow :
chmod +x fastqt-0.2.3-linux-x86_64.AppImage
./fastqt-0.2.3-linux-x86_64.AppImage
### Archlinux
There is an AUR package for Archlinux. [Just get it from the AUR](https://aur.archlinux.org/packages/fastqt/).
### Windows
Windows installer and portable version are avaible [here]( https://github.com/labsquare/fastQt/releases/)
## Compilation
### Prerequisites - Install KArchive
On Linux, you need to install karchive before compiling FastQt.
**From ubuntu** >xenial you can install it from repositories :
sudo apt install libkf5archive-dev
**From fedora** >= 24 you can install it from repositories :
sudo dnf install kf5-karchive-devel
**From source** :
git clone git://anongit.kde.org/extra-cmake-modules
cd extra-cmake-modules
mkdir build && cd build
cmake .. -DCMAKE_INSTALL_PREFIX=/usr/
make && sudo make install
cd ../..
git clone git://anongit.kde.org/karchive.git
cd karchive
mkdir build && cd build
cmake .. -DCMAKE_INSTALL_PREFIX=/usr/
make
sudo make install
** From Windows **
Nothing to do. Compiled library are avaible in win32 directory.
### Install Qt >5.7
**From website** : Download Qt > 5.7 from https://www.qt.io/.
Don't forget to check QtChart module during installation.
**From ubuntu** : Qt 5.7 is not yet avaible with ubuntu. But you can add PPA to your software system.
For exemple from xenial
sudo add-apt-repository ppa:beineri/opt-qt57-xenial
sudo apt-get install qt57base qt57charts-no-lgpl
source /opt/qt57/bin/qt57-env.sh
**From fedora** : Qt 5.7 is avaible
sudo dnf install qt5-qtbase-devel qt5-qtcharts-devel
### Compile FastQt
Be sure you have the correct version of Qt (>5.7) by using qmake --version. For exemple, if you have installed Qt from ppa:beineri, you will find it under /opt/qt57/bin/qmake. Then launch the compilation from FastQC folder as follow.
/opt/qt57/bin/qmake --version
/opt/qt57/bin/qmake
make
sudo make install
## Usage
FastQt can analyse uncompress and compress fastq files. The following extensions are supported :
- *.fastq
- *.fastq.gz
- *.fastq.xz
- *.fastq.bz2
You can use FastQt as GUI application or as a Command Line Interface.
Some usage example :
```
fastqt file1.fastq # File is save in file1 directory
fastqt file1.fastq file2.fastq.gz file3.fastq.bzip # File save in file1 file 2 file3 directory
fastqt file1.fastq -o specific_path # Create specific directory for each file in specific_path
fastqt file1.fastq -t 2 # Fastqt run maximal two process this option is valid for GUI too
```
## How to cite FastQt
Labsquare Team, et al (2017). FastQt: a quality control tool for high throughput sequence data. Available online at: https://github.com/labsquare/fastQt