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File formats

Data is only as good as the format it is saved in. The format of a file determines which programs can be used to access it.

Open vs Proprietary

  • Can be opened by anyone using different types of open-source, free or licensed software.
  • Are less prone to become obsolete, because a variety of software should be able to open them.
  • Have a free format specification (i.e. no patent restrictions).
  • List of open formats.

Files in PROPRIETARY format (non-preferred)

  • Can only be opened using paid-licence software.
  • Tend to be replaced by new versions or new formats, limiting their future reuse.
  • Have an either patented or trade-secret specification.
  • List of proprietary formats.

Considerations before choosing a file format

  • The format of raw and processed data files could depend on the instrument or the software that generates the data.
  • Some data repositories could require specific file formats. In this case, information about the accepted formats can be found on the repository‚Äôs webpage.
  • It is good practice to use open or recommended formats when possible.

Is my file format open?

Area Technology Format Open
Genomics Sequencing fastq yes
Proteomics Mass spectroscopy mzXML or mzML yes

Sources and further reading