I would not have expected such a misunderstanding of the fruits of the knowledge of the human reference sequence from J Craig Venter. Frankly, it sounds like so

I would not have expected such a misunderstanding of the fruits of the knowledge of the human reference sequence from J Craig Venter. Frankly, it sounds like sour grapes. For some reason, I feel inclined to try to explain some of the technical reasons why the public project's approach was necessary for the completion of the human genome. There is broad agreement (perhaps "universal - 1") that Venter's sequencing approach would never have been able to achieve the level of completeness that we have now thanks to the Human Genome Project. This is because of duplicate DNA in the human genome, and the nature of short read lengths. Let's try this with colors. Say you have a terrible sequencer that only reads 7bp at a time, max. You come across the following 2 strands of DNA: GREENgattacaGREEN REDgattacaRED They're on 2 entirely different chromosomes, but you don't know this since there exists no reference sequence - you're mapping de novo, remember? Good. So you're get readouts like "GREENgattac" and "gattaca" and "attacaRED" - but you don't have any reads >7bp, so you never see what is on both sides of gattaca at once. Thus, since you can never span gattaca, you will never know if your DNA in this region should be GREENgattacaRED + REDgattacaGREEN, or REDgattacaRED + GREENgattacaGREEN. For de novo alignment with short reads, this type of shortcoming is deadly. Because the public consortium / Human Genome Project used much longer read lengths and a method involving bacterial artificial chromosomes, they were able to map the more difficult regions of the genome having repeats. Edit I should have addressed the public consortium's approach more thoroughly, though to be clear I am less familiar with the approach and have never used it myself. Essentially, you chop up the 3 gigabase genome into a bunch of 150 kilobase segments (in this case, bacterial artificial chromosomes). You can map these back to their source chromosomes, of which we already knew we had 23. You then chop these BACs up into smaller pieces and sequence. In the worst case, you might be unsure of where some of your reads from each BAC map within the 150kb window that they come from, but hey, at least you know which chromosome and more or less which portion of the chromosome they come from. In other words, in the situation described above, the RED and the GREEN never co-occur, since they are on different BACs and are not sequenced together. Thus you know that RED/RED and GREEN/GREEN are the right pairings (and you know which belongs on which chromosome).