College of Public Health

Information Technology

How to Install FastQ Screen on Ubuntu 18.04

Article ID: KB48563

Install Miniconda2

  1. wget https://repo.anaconda.com/miniconda/Miniconda2-latest-Linux-x86_64.sh
  2. bash Miniconda2-latest-Linux-x86_64.sh
  3. Accept the EULA
  4. Accept the default install location
  5. Respond with yes to initialize Miniconda2 (the default response will be no)
  6. Restart or log out and log back in to refresh your environment variables
  7. Verify the installation by running conda update conda

Install Bowtie 2

  1. conda config --add channels bioconda
  2. conda create --name bowtie2 --clone base
  3. conda activate bowtie2
  4. conda install bowtie2

Download FastQ Screen

  1. Open https://www.bioinformatics.babraham.ac.uk/projects/download.html#fastqscreen and determine the latest version number of FastQ Screen. These instructions will install version 0.13.0. Simply replace 0.13.0 with the latest version number to install the latest version of FastQ Screen.
  2. wget https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/fastq_screen_v0.13.0.tar.gz
  3. tar -xvf fastq_screen_v0.13.0.tar.gz
  4. rm fastq_screen_v0.13.0.tar.gz

Add FastQ Screen to PATH

  1. echo 'export PATH="$PATH":/home/'$USER'/fastq_screen_v0.13.0' >> ~/.bashrc
  2. Restart or log out and log back in to refresh your environment variables

How to run FastQ Screen

  1. conda activate bowtie2
  2. Modify fastq_screen.conf as needed (nano fastq_screen_v0.13.0/fastq_screen.conf)
  3. fastq_screen --help

Install Perl GD library to draw graphs with FastQ Screen (Optional)

  1. sudo apt install -y libgd-graph-perl (the sudo command will require your password)

Test FastQ Screen (Optional)

  1. wget https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/fastq_screen_test_dataset.tar.gz
  2. tar -xvzf fastq_screen_test_dataset.tar.gz
  3. rm fastq_screen_test_dataset.tar.gz
  4. gunzip fastq_screen_test_dataset/fqs_test_dataset.fastq.gz
  5. fastq_screen --get_genomes (the genomes will take a significant amount of time to download)
  6. cp FastQ_Screen_Genomes/fastq_screen.conf fastq_screen_test.conf
  7. sed -i 's|/bi/scratch/wingetts/FASTQ_Screen_Paper/FastQ_Screen_Genomes/||g' fastq_screen_test.conf
  8. fastq_screen fastq_screen_test_dataset/fqs_test_dataset.fastq --aligner=Bowtie2 --conf=fastq_screen_test.conf

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