Hi!

I have a pile of unindexed reads, including some PhiX, from a poor run on a NexSeq. Can anyone suggest some tools or techniques I can apply to this data just to try get a better idea of why the run went poorly?

Much appreciated.
You could try blasting a few reads to get an idea whether it's poor quality, PhiX,...
There will be more sophisticated methods for sure but it's a start :)