FastQC

FastQC is a reliable quality control tool designed to help you verify the throughput sequence files and export the result in FastQ format. In other words, you can view and analyze data from sequenced files, then export it as a special format that supports all the base calls for both encoded and simple sequences.

FastQC allows you to load information from various types of sequence files, FastQ or Casava FastQ documents. Moreover, you can load all the entries from BAM/SAM files or select only the mapped ones.

The program can only read the information from a single file, at once, but it allows you to open several entries and easily switch between them. The side panel displays the analysis categories, along with the base call used for each one. You can thus view the Base Statistics, Sequence quality per base or per sequence.

FastQC allows you to view the sequence content per base or the GC content per sequence, N content per base, Sequence Length Distribution or Sequence Duplication Levels. You may view Overrepresented sequences, the Adapter content and Kmer content.

The base statistics and overrepresented sequences are displayed as data in tables, whereas the other parameters are depicted as line graphs.

The analysis performed by FastQC is to verify that the raw data in the sequence files is correctly written; there are no issues or biases that could affect the further uses of the data. The program can also generate comprehensive reports that allow you to spot problems early on.

FastQC allows you to easily generate reports based on the quality verification, by selecting the dedicated control from the File menu. The report can help you identify problems stemming in the sequencer or the starting library material. The program can be used as a standalone tool or integrated into systems suitable for larger file analysis pipelines.