[new299]

I’ve done this:

https://aseq.substack.com/p/bringing-up-an-old-ebay-miseq

Your issues are that you will still need to purchase reagents from the sequencing instrument vendor. They will try and push you toward a service contract.

Each kit will cost ~$600 (cheapest kit) an old Illumina sequencer which you can still buy reagents for will cost at least $5000.

Doing a whole genome this way would be expensive… I’d guess $10K to $20K perhaps? You’d need a lot of kits… or one of the high spec sequencers (NextSeq 550 etc).

Alternatively you could look at getting a nanopore sequencer. This will be cheap but the data quality is different (and may not be comparable/require high coverage for certain applications). I’d guess you could do a (30x) whole genome for <$10K all inc here?

[derefr]

Ah, but what if you were also a biochemist, and so you wanted to vertically integrate your amateur gene lab by making your own reagents? Because I'm guessing that those $600 kits don't really have a $600 BOM...

[new299]

No, but creating these reagents is a lot of work.

Principally create new flowcells coated with an oligo lawn would be difficult. Not impossible… but a non-trivial project…

[darkerside]

What makes nanopore screening quality worse? Aren't these long read sequencers that are supposed to read more of the DNA strand?

[jhbadger]

The problem with Nanopore (which I've used for some projects) is that the per-base accuracy is still quite low. This can be helped to a degree by either high coverage (basically sequencing the same area over and over again with the hope that the errors are stochastic and will be corrected if you take the "average" base at each position) or combining it with shorter read but higher quality data from Illumina.