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QUality ASsessment Tool for Genome Assemblies

Project web page

As of the moment of writing this, the latest stable version QUAST 5.0.2 contains a known bug AttributeError: module 'cgi' has no attribute 'escape'. It's suggested to use pre-release QUAST 5.1.0 RC1 where this bug is fixed.

Ubuntu 20.04

sudo apt install -y zlib1g-dev pkg-config libfreetype6-dev libpng-dev python3-matplotlib
cd ~
wget https://github.com/ablab/quast/releases/download/quast_5.1.0rc1/quast-5.1.0rc1.tar.gz
tar -xzf quast-5.1.0rc1.tar.gz
rm ./quast-5.1.0rc1.tar.gz
cd ./quast-5.1.0rc1

Now, edit the setup.py script as sudo nano ./setup.py

  • find the first line: #!/usr/bin/env python
  • and replace it with: #!/usr/bin/env python3
# install
sudo ./setup.py install_full
# test installation
./setup.py test

Fedora 33

# Install prerequisites
sudo dnf install -y python3-matplotlib freetype freetype-devel zlib-devel pkgconf-pkg-config libpng-devel

wget https://github.com/ablab/quast/releases/download/quast_5.1.0rc1/quast-5.1.0rc1.tar.gz
tar -xzvf quast-5.1.0rc1.tar.gz
cd ./quast-5.1.0rc1

Installer is supposed to use Python 2, which is deprecated. To force use of Python 3, edit the ./setup.py script:

  nano ./setup.py

And edit the first line:

#!/usr/bin/env python

to run with Python 3:

#!/usr/bin/env python3

Run and verify installation:

sudo ./setup.py install_full
./setup.py test

By defaults, it installs itself to /usr/local/bin, no need to keep installation files:

cd ~
sudo rm -rf ./quast

To check if it can run from any location:

wget quast.sf.net/test_data.tar.gz && tar -xvzf test_data.tar.gz
quast.py --test