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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