Currently, the FastQC software (Babraham Bioinformatics) provides the most convenient way for:
- Preliminary quality check of raw sequence data obtained on Illumina, BGI and Ion Torrent platforms
- Calculating a percent of duplicated reads (duplication rate)
- Visualizing the distribution of reads length and nucleotide content
- Calculating and visualizing GC distribution over bases/reads
- Extracting overrepresented sequences from a fastq file
# Download and unzip the latest release of FastQC software:
wget https://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.9.zip
unzip fastqc_v0.11.9.zip
# Make the fastqc running script executable:
cd FastQC
sudo chmod 755 fastqc
# Create a link in your $PATH (e.g. /usr/local/bin):
sudo ln -s /path/to/FastQC/fastqc /usr/local/bin/fastqc
# Launch interactive interface from any location:
fastqc
# Or, apply to one or multiple fastq files from any directory:
fastqc file1.fastq file2.fastq .... fileN.fastq
