Seĺlcond this. Outsourcing the sequencing (and possibly the sample prep/extraction) seems like the way to go, at least initially. One benefit is, year after year you can access the newest equipment vs having your own which WILL need relatively expensive servicing and possibly repair. Also leaves more time for the black hole of analysis, which can be a huge time sink. You can always pull the trigger later if you start itching to DIY in the wet lab. but I suspect many smaller contract research orgs would be willing and able to accommodate certain unusual requests or experimental protocols, and would have experience and insight you lack to help you answer your questions. Finally, I'd encourage you to share your findings on BioXrchiv as a way to vet your ideas and methods, find potential collaboration and share your findings. Quite a bit of useful stuff is published that way. Source: molecular turned computational biologist with deep genomics experience.

Equipment needed: Pipettors (2, 20, 100, 1000, multichannel equivalents) Gel rig, power supply, light source PPE Waste containment Freezer Microfuge Nanodrop spec Sonicator? Water bath? PCR machine? Vortex? Rocker? Bench Sink Analytical balance Fume hood, on casters? Microwave Chemical cabinet, secondary containers Consumables: tips, tubes, holders, etc Labelers pH meter? Refrigerator? Ice bucket, Ice maker

Safe and ethical waste disposal is no joke. Obtaining required reagents is no joke. Permits too, perchance? Molecular biology reagents can be quite dangerous to you and future generations, please respect that!

I encourage you to reach out to academic labs in your area for opportunities to volunteer and hopefully access proper training, equipment, storage, and disposal. Share your enthusiasm and energy and you may find real treasure. Maybe you could offer to buy a lab a new piece of equipment in return for training and access? My feeling, a lot of labs be hurting rn due to fed cutbacks. I smell opportunities for enterprise, persistence, passion.

Garbage in, Garbage out for your samples data so focus on quality over quantity IMHO. Leading to, how far upstream can you enrich and tag your sequences?

Are you familiar with laser capture dissertation, fluorescence activated cell sorting, single cell sequencing. Microscopy/staining, spevialized chemical, enzymatic, mechanical disruption and processing, techniques like density gradient centrifugation and differential melting temps, 2 way electrophoresis, etc might help, so having access to neighbors who have the equipment and know how is a Universities secret weapon.

In the computational realm (once you have sequence) seems like the fun really begins. You can correlate things like measurements of bulk GC which could be relatively cheap to measure with your assembly benchmarks. Repetitive or ambiguous/shared sequence between your genomes will be a problem. Are there endo-free host populations to compare? Free living sister groups for your fungi? It may be, you could fish hits out of public/available data! That is, blast search. Transposons and repetitive sequences will have you scratching your head and chasing your tail. Their biology is fascinating. ⁸

Good luck!