Coffa files (.coffa) contain the demultiplexed sequencing output and several analysis properties of a single digitalMLPA reaction. These files are produced in the first steps of the data analysis using data from the FASTQ file(s). As Coffa files are relatively small (typically <1 MB), they are a convenient alternative to FASTQ files to store or transfer the results from a digitalMLPA experiment. They contain all the information required for the data analysis by Coffalyser digitalMLPA.

Coffa files can be generated with a command line tool. This can be useful for NGS service providers that pool digitalMLPA experiments from several end users in a single sequencing run, as this allows the service provider to supply each end user with the sequencing output of their own experiment. The end users can continue the analysis of their own experiment(s) with Coffalyser digitalMLPA. The Coffalyser digitalMLPA User Manual contains instructions on how to use the command line for this purpose.