FastQC

FastQC is a handy quality control tool that helps you check the quality of your sequence files. It lets you see and analyze data from sequenced files and then export it in FastQ format, which is great for handling base calls for both encoded and simple sequences.

Loading Different Types of Sequence Files

With FastQC, you can load info from different kinds of sequence files, like FastQ or Casava FastQ documents. You can even pull all entries from BAM/SAM files or just the mapped ones. This flexibility makes it super useful!

Easy Navigation Through Files

The program reads one file at a time but lets you open multiple entries and switch between them easily. On the side panel, you'll find analysis categories along with the base call used for each one. You can check out Base Statistics, Sequence Quality per base, or even per sequence.

Analyzing Sequence Content

FastQC allows you to look at the sequence content per base, GC content per sequence, N content per base, Sequence Length Distribution, and even Sequence Duplication Levels. Plus, you can check out Overrepresented Sequences, Adapter Content, and Kmer Content!

Data Visualization

The results are shown in tables for base statistics and overrepresented sequences while other parameters are displayed as line graphs. This makes it easy to spot trends and issues in your data.

Generating Reports for Better Insights

The main job of FastQC is to make sure that the raw data in your sequence files is accurate—no issues or biases that could mess things up later on. It can create detailed reports that help you catch problems early.

User-Friendly Reporting Features

You can quickly generate reports based on your quality checks by picking the right option from the File menu. These reports are super helpful for spotting issues with your sequencer or starting library material. Whether you're using it alone or integrating it into larger file analysis systems, FastQC has got you covered! If you're ready to give it a try, download FastQC here!