FastQC-0.11.5 (multi-file)



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Please work through the documentation and add your comments on the bottom of this page, or email comments to Thank you.


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


NOTE: FastQC will determine the format that your FASTQ reads are in (PHRED33, Illumina, etc). The detected read type will be listed on the graphs outputted. As an additional note, PHRED33 is exactly the same as Solexa / Illumina 1.9, thus if using these FASTQ files in downstream apps such as the FASTX toolkit, you will need to select PHRED33 for your format type if your reads are in Solexa/Illumina 1.9 format.

Test Data

All files are located in the Community Data directory of the iPlant Discovery Environment at the following path:

Community Data > iplantcollaborative > example_data > fastqc

Input File(s)

Use SRR070572_hy5.fastq as test data.

Output File(s)

All outputs can be found in the directory Community Data > iplantcollaborative > example_data > fastqc

  • Expect the following as outputs (in addition to the logs generated for all analyses)
    • Directory with name of the input file used
    • zipped instance of this directory
  • Within the directory generated (in the case of the above example, it should read SRR070572_hy5_fastqc), there are two sub directories and several files.
    • Sub directories are icons (not scientifically necessary) and images.
    • Files generated in this directory are the following: fastqc_data.txt, fastqc_report.html and summary.txt
  • Within the image directory, the following files should be available:
    • duplication_levels.png
    • kmer_profiles.png
    • per_base_gc_content.png
    • per_base_n_content.png
    • per_base_quality.png
    • per_base_sequence_content.png
    • per_sequence_gc_content.png
    • per_sequence_quality.png
    • sequence_length_distribution.png

Tool Source for App