HTML reports
Alongside the text report, fastp also creates a human-readable HTML report (fastp.html), and a JSON report (fastp.json) meant to be analyzed by a program (more on that in a bit):
Let’s open up this HTML report in a new tab:
At the top of the HTML file, you’ll find the same stats we saw in the previous step, but the rest of the file contains interactive plots showing, for example, how the base quality changes as a function of the position along the read.
Note that the y-axis does not start at 0 so the decrease in quality looks more pronounced than it actually is; in fact, the base quality is > 30 across the length of the read, which is excellent!
The open command will also work on MacOS, but on Linux systems, you can use xdg-open instead.