FastQC Quality Control

FastQC aims to provide a simple way to do some quality control checks on raw sequence data coming from high throughput sequencing pipelines. It provides a modular set of analyses which you can use to give a quick impression of whether your data has any problems of which you should be aware before doing any further analysis.

The main functions of FastQC are

• Import of data from BAM, SAM or FastQ files (any variant)

• Providing a quick overview to tell you in which areas there may be problems

• Summary graphs and tables to quickly assess your data

• Export of results to an HTML based permanent report

• Offline operation to allow automated generation of reports without running the interactive application

See the FastQC home page for more info.

To run FastQC on our data, simply type:

cd /mnt/WGS-data
fastqc read1.fq read2.fq

After FastQC finished running you can access the report using a web browser:

firefox *.html

Check out the FastQC home page for examples of reports including bad data.

• Quality Treatment
• Run fastp on a PE library
• Run FastP again
• Trimming adapter sequence