Thursday, 16 June 2016

FastQC tool

FastQC is a quality control tool for checking the quality of raw reads obtained from Next Generation sequencing platforms. It provides a modular set of analysis which gives a quick hint of quality of your data. It generates QC report in the form of graphs showing quality, N content, Adapter content, GC content present in your high throughput sequencing data. It can be downloaded from (
FastQC can be run in different modes which are
  • Standalone interactive application
  • Non interactive mode
  • By using galaxy which contains integrated FastQC tool


1) Install the FastQC from above mentioned link. It can be installed on both LINUX as well as windows operating system. on linux it can be installed by using command 
         sudo apt-get [link of fastQC from where you are downloading]
sudo ln -s /path/to/FastQC/fastqc /usr/local/bin/fastqc
fastqc somefile.txt
2) After installing FastQC now simply run the program and select File > Open. You can then select the files you want to analyse by using windows. But in LINUX use following command
fastqc somefile.txt
FastQC supports files in the following formats
  • FastQ (all quality encoding variants)
  • Casava FastQ files*
  • Colorspace FastQ
  • GZip compressed FastQ
  • SAM
  • BAM
The analysis in FastQC is performed by a series of analysis modules. The left hand side of the main interactive display or the top of the HTML report show a summary of the modules which were run, and a quick evaluation of whether the results of the module seem entirely normal (green tick), slightly abnormal (orange triangle) or very unusual (red cross).
Shown below are some results obtained from FastQC

Summary report FastQC

Now after generation of report click on the options showing on left of the windows to get other details like N content, Adapter content, GC content and many more in graphical format. The quality control step is the first step of Next Generation Sequencing data analysis. These graps shows the complete report about quality of the raw reads. Any reads that do not meet the quality are Trimmed off Using any of the poor quality reads trimming tools. To know about the trimming tools stay connected and visit the blog.