Testing for viral/bacterial infection FASTQ files What's the best way to test if a pair of Illumina FASTQ files from blood DNA extraction contain any reads from viral/bacterial infection from DNA in human blood? Thanks in advance.

EDIT:

Looking at the available options, I started testing Kraken for samples where I have seen an indication of viral reads, I will update with results / further questions.
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.