JSON reports

fastp also outputs a fastp.json report:

Let’s say you’re running fastp as part of an analysis pipeline, and you want to make an automated decision about what kind of analysis to run depending on data quality. In that scenario, it’s a lot easier to parse this JSON file programmatically than any of the other outputs we’ve seen so far.

For example, to extract summary statistics from the report, we can use the command-line tool jq:

Or to extract the number of reads that were filtered out because they had too many N’s in their sequences: