45 lines
2.2 KiB
Plaintext
Executable File
45 lines
2.2 KiB
Plaintext
Executable File
FastQC - A Quality Control application for FastQ files
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Most high throughput sequencers generate output in FastQ format. This
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format combines the base calls for the sequence which was generated with
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an encoded quality value for each base which says how confident the
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sequencer was that the base call generated was correct.
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Before proceeding with the analysis of a sequence data set it is
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a good idea to do some basic quality control checks on the raw data
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to ensure that there are no hidden problems which might be more
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difficult to detect at a later stage.
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FastQC is an application which takes a FastQ file and runs a series
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of tests on it to generate a comprehensive QC report. This will
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tell you if there is anything unusual about your sequence. Each
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test is flagged as a pass, warning or fail depending on how far it
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departs from what you'd expect from a normal large dataset with no
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significant biases. It's important to stress that warnings or even
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failures do not necessarily mean that there is a problem with your
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data, only that it is unusual. It is possible that the biological
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nature of your sample means that you would expect this particular
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bias in your results.
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FastQC can be run either as an interactive graphical application
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which allows you to view results for multiple files in a single
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application. Alternatively you can run the program in a non
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interactive way (say as part of a pipeline) which will generate
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an HTML report for each file you process.
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FastQC is a cross-platform application, written in java. In theory it
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should run on any platform which has a suitable java runtime environment.
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Having said that we've only tested in on Windows, MacOSX and Linux
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running the Oracle v1.6 to 1.8 JREs. Please let us know what happened if
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you try running it on other platforms / JREs. Please see the detailed
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instructions in the INSTALL.txt document to tell you how to get a
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suitable java version to run FastQC on your system.
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If you have any comments about FastQC we would like to hear them. You
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can either enter them into the github bug tracker at:
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https://github.com/s-andrews/FastQC/issues/
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..or send them directly to simon.andrews@babraham.ac.uk.
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