Testing for viral/bacterial infection FASTQ files
If you're talking RNA, I have a blog post from a while back about Diamond/MEGAN:

http://achri.blogspot.com/2017/04/data-for-free-viral-metagenomics-in.html

In principle this will work for DNA if you have a non-trivial number of pathogen reads (since they tend to be gene dense in their genomes). Otherwise I use Kraken on a database for all the NCBI nt database, but this is slower and doesn't let you sanity check the false positive taxonomy assignments as well as I describe in the post. Of course, ideally, you run multiple methods if you have the resources to do so.