The field of human genetics had a landmark year in 2001. Two groups published a draft sequence of the human genome at the same time (1, 2). One paper was from the International Human Genome Project (HGP) (1), a public group that provided open access to their sequence as it was obtained. The other paper was authored by a private group, Celera Genomics (2), who do not provide immediate or free access to their sequence data. Accordingly, Celera used both the publicly available data and their independently generated data in compiling their draft of the human genome. The public group used a conservative, divide-and-conquer strategy in which segments of the genome were first cloned into bacteria to yield bacteria artificial chromosomes (BACs). These BACs were mapped and then sequenced. The private group used a bolder, whole-genome shotgun (WGS) method in which genome-wide sequence fragments are assembled computationally. In March of 2002, Waterston, Lander, and Sulston, leaders in the HGP, claimed that the public data played a critical enabling role in the Celera assembly (3). They argued that Celera's highly ordered shredding of the HGP data preserved so much of its long-range assembly that the Celera assembly was not independent and was not achieved by the WGS method. PNAS invited two commentaries on this paper. One, by Green (4), concluded that because Celera's work was anchored by sequence islands obtained from the public database, the assembly reported by Celera could not be viewed as a true WGS assembly. The second commentary, by some of the leaders of the Celera initiative (5), strongly disagreed with the allegations. They argued that Celera started with shredded bactigs and not with reassembled HGP data. They also criticized the simulation Waterston et al. used to support their argument and said it was based on incorrect and oversimplified assumptions. From the feedback PNAS received after the publication of these papers, it was clear that the views presented were so divergent that it was very difficult for the scientific community to evaluate the claims. The exact areas of disagreement were not even clear. The major issues in the disagreement were submerged in the incompatible claims. The controversy is not about the validity of the WGS method for sequencing very large genomes, but about whether Celera used this method to assemble the human genome in 2001. If their results depended on the HGP, which is derived from a hierarchical method, then they did not assemble an independent draft sequence. There is no problem in Celera using the HGP data; it was there for everyone. The disagreement is in how it was used. Was it shredded so well that it only provided additional sequence reads to supplement the extensive ones by Celera? Or was much of the sequence integrity retained? There is also no question that Celera produced a high-quality draft. The question is only whether the long-range assembly was independent. Accordingly, we thought that one more round of comments would clarify the situation. Representatives from both the public HGP group and the private Celera group agreed to author a second and final round of perspectives. These papers can be found on pages 3022 and 3025 (6, 7). We used the following ground rules for these invited papers. In the first round, because the HGP group initiated the debate (3), we provided Celera an advance copy of the HGP paper so they could prepare their rebuttal commentary (5). We did not show the rebuttal to the HGP group. This second round of the debate has followed similar protocol. The HGP contribution (6), which addresses the first response by Celera and provides new arguments, was sent to Celera for their reply (7). We felt that Celera should have the last word as it was their assembly that was being questioned. Accordingly, the HGP authors did not see, and thus could not comment on, the Celera response. We asked both groups to stick to the scientific issues, to avoid recrimination, and to explain technical terms clearly. Both contributions were reviewed and revised. We believe that this second round of the debate has clarified the issues surrounding this epoched contribution to science.