Hmmm, isn't deep learning starting to pick up for genetics? No idea if it is actually is, but everyone in DL seems to be talking about it, I thought I'd ask someone actually in bioinformatics :)
I wish I could say, I it's been a good two+ years since I left the genetics company, so I've been in a different industry for a while. I would say theres probably plenty of room, if people start taking more novel approaches that use more data, eg, full microbiome analysis. Also, I was just a sysadmin, so I don't really know anything other than keeping systems running, so take what I say with a grain of salt.
I suspect DL will have a limited to modest role in the actual search / alignment part, and a lot more to do with the analysis part. This includes medical diagnosis, identifying regulatory patterns based on high throughput expression data, such stuff.
Not necessarily in comp. genetics / sequencing.. / the DNA stuff..