It was a fairly big controversy at the time, because it wasn't clear you could do shotgun assembly of a genome the size of the human genome without the scaffolding that the official project put in place, and also...the company was trying to get the genome "first" so that it could file patents. It all seems a little quaint now, given how little immediately actionable information came out of the genome effort, but it was the OpenAI vs Anthropic of the late 90s.
Also, for what it's worth, my recollection is that the Venter genome is actually...Craig Venter's genome.
The main controversy was indirect, e. g. several actors - including Craig - trying to patent ESTs. That scaffolding was possible was already shown before, e. g. Haemophilus influenzae in 1995: https://pubmed.ncbi.nlm.nih.gov/7542800/
Shotgun assembly was not as controversial, just a more efficient divide-and-conquer approach that was mostly new-ish at the time.
> It all seems a little quaint now, given how little immediately actionable information came out of the genome effort
Well - you have the sequence, but the sequence alone does not necessarily tell everything. You just have more information than before.
You're under-selling it. Celera filed thousands of patents on expressed sequence tags, long before anyone knew anything about them. It was a land grab.
Also, it only seems obvious if you're looking back at it with 20+ years of hindsight, but it was quite unclear at the time if it was possible to obtain a full read of the genome from shotgun sequencing alone. The human genome is 3000x larger than H. influenzae, and significantly more complex.
The end of this short interview with Stuart Schreiber has a similar vibe:
https://www.nature.com/articles/s41570-026-00803-0
Note how interested he is in consciousness and AGI. This is something that he's been talking about for a long time, just formulated differently. You need to be able to temper true scientific rigor with a little bit of wackiness to even think about tackling these big questions.
Venter was the enemy of the Human Genome Project, he swept in late, after much discovery had been made and technology developed, and most of the data was generated. And he was going to add a tine bit of new data and then patent it so that the dream of a publicly usable human genome was impossible.
Venter was an important figure that did many good things, but his involvement with the human genome was entirely negative.