This paper brings forward a de novo genome genome of the olive baboon assembled using 10x, ONT (Nanopore), HiC and BioNano maps corrected for the large assemble errors with Panu_3.0, leading to an improved genome annotation. This data is valuable as the previous baboon assembly based on the Illumina short reads and mate pairs was a lot more fragmented. A nice feature was to infer the recombination rate and annotating the crossover breakpoints. The resulting genome reaches 2.87 Gb of continuous sequence with less than 0.1% of uncalled bases (gaps), and a 10 times improved N50 containing 93 complete genes according to BUSCO

There are some issues with the presentation of date in this version of the paper, as some of the data is missing (repeats) not presented (ONT), and some should be clarified (BUSCO scores, Tables 1 and 2).
1. This investigation would greatly benefit from description of the repeats. Isn't is the whole point of using long read data? 2. BUSCO score is lower in their final assembly. This is strange, and needs to be addressed somewhere. 3. While the assembly has benefited from the 15x ONT coverage, i was not able to find information on the reads. The authors used the ONT data to assemble scaffolds with LR_Scaf (published as recently as last December) and calculated gap lengths. In LRScaf paper - the authors mention that the benefits of their method is speed and resource consumption. Therefore, it is not clear why there were not used for assembly, only for scaffolding with no justification given.
4. Table 1 and 2 should be combined, just add the last column of Table 2 to the end of table 1, there is no reason to report the Panubis 1.0 statistics twice. 5. Finally, I am a little concerned with continuous classification of animals according to their biomedical need, rather with their evolutionary and ecological significance. This trend is recently prevalent in GigaScience as well as the other journals and reflect an extreme anthropocentric view. I think that the paper will benefit from a statement on how this data contributes to the completeness of the primate research, evolutionary, comparative and conservation studies.

Declaration of competing interests Please complete a declaration of competing interests, considering the following questions: Have you in the past five years received reimbursements, fees, funding, or salary from an organisation that may in any way gain or lose financially from the publication of this manuscript, either now or in the future? Do you hold any stocks or shares in an organisation that may in any way gain or lose financially from the publication of this manuscript, either now or in the future? Do you hold or are you currently applying for any patents relating to the content of the manuscript? Have you received reimbursements, fees, funding, or salary from an organization that holds or has applied for patents relating to the content of the manuscript? Do you have any other financial competing interests? Do you have any non-financial competing interests in relation to this paper? If you can answer no to all of the above, write 'I declare that I have no competing interests' below. If your reply is yes to any, please give details below.

I declare that I have no competing interests.

I agree to the open peer review policy of the journal. I understand that my name will be included on my report to the authors and, if the manuscript is accepted for publication, my named report including any attachments I upload will be posted on the website along with the authors' responses. I agree for my report to be made available under an Open Access Creative Commons CC-BY license (http://creativecommons.org/licenses/by/4.0/). I understand that any comments which I do not wish to be included in my named report can be included as confidential comments to the editors, which will not be published. I agree to the open peer review policy of the journal.

Authors' response to reviews: Reviewer #1:

• Reference style is not identical, examinations are needed.

We have corrected the reference style to reflect the instructions provided to authors on the GigaScience website.

• Both package versions and parameter settings of the software used should be given.

We have updated the text to include the package versions and parameter settings of software that have been used.

• In my view, during the assembly process, the Nanopore long-reads should be polished by lllumina paired-end reads firstly.

We communicated with the author of LR_Gapcloser, which is the tool we used to scaffold the contigs with nanopore long reads.

We asked them the following question: "Would you recommend using raw nanopore reads or error-corrected nanopore reads. If you suggest error-corrected nanopore reads, would you suggest self-correction or correction with illumina reads?

The author responded with: "——Directly use the raw reads...We found that using the uncorrected read has better performance than using the corrected reads."

Consequently, we used the raw Nanopore long-reads.

• The figure legend of the Hi-C heatmap need to be improved, some details are missing.

We have modified the figure legend of the Hi-C heatmap to provide additional details.

• I can not understand the meaning of the Fig.3. What is the reader supposed to conclude from the figure?

We have modified the figure legend for Figure 3 to describe the motivation behind it. In particular, we wanted to demonstrate why we believe that the scaffold labeled chromosome Y by us, is putatively at least a part of the true chromosome Y of the genome, by showing that chromosome Y synteny between Panubis1.0 and rhesus is similar to the chromosome Y synteny between human and chimp.

• The genome completeness assessment shows that the completeness of Panu_3.0 is better than that of Panubis1.0 (93.4% Vs 93%), please explain this.

We performed an updated BUSCO analysis using the Euarchontoglires gene set instead of the broader Mammalia gene set provided by BUSCO. We have updated the manuscript to show that the number of “Complete” genes found in Panubis1.0 and Panu_3.0 is almost identical.

• It would be good for the authors to explain how they have addressed the main problem with the HiC for the accurate orientation of the inversions within the scaffolds.

We thank the reviewer for their comment. We have added an explanation of how we have addressed the main problem with Hi-C data of the accuracy of orientation of short contigs, within the discussion section. In particular, since our contig N50 is > 1 megabase and the orientation accuracy of contigs with Hi-C data increases with contig length, this should not be a big problem for our dataset.

Reviewer #2:

There are some issues with the presentation of data in this version of the paper, as some of the data is missing (repeats) not presented (ONT), and some should be clarified (BUSCO scores, Tables 1 and 2).

We have tried our best to incorporate these suggestions into the manuscript.

• 1. This investigation would greatly benefit from description of the repeats. Isn't is the whole point of using long read data?

We have included an analysis of repeats for Panubis1.0 as well as Panu_3.0 using the RepeatMasker software.

• 1. BUSCO score is lower in their final assembly. This is strange, and needs to be addressed somewhere.

We have added a refined analysis of the BUSCO scores to the manuscript using the Euarchontoglires gene set instead of the broader Mammalia gene set provided by BUSCO. We have updated the manuscript to show that the number of “Complete” genes found in Panubis1.0 and Panu_3.0 is almost identical.

• 1. While the assembly has benefited from the 15x ONT coverage, i was not able to find information on the reads. The authors used the ONT data to assemble scaffolds with LR_Scaf (published as recently as last December) and calculated gap lengths. In LRScaf paper - the authors mention that the benefits of their method is speed and resource consumption. Therefore, it is not clear why there were not used for assembly, only for scaffolding with no justification given.

The Canu assembler documentation (which can be found at https://canu.readthedocs.io/en/latest/quick-start.html) recommends that "For eukaryotic genomes, coverage more than 20x is enough to outperform current hybrid methods, however, between 30x and 60x coverage is the recommended minimum." Since we only had 15x nanopore reads, we consequently didn't attempt to assemble the nanopore reads de novo and opted to use them for scaffolding of contigs instead. We have also modified the discussion section to provide this reasoning.

• 1. Table 1 and 2 should be combined, just add the last column of Table 2 to the end of table 1, there is no reason to report the Panubis 1.0 statistics twice.

We have modified Table 1 and Table 2 and combined them into a single table.

• 1. Finally, I am a little concerned with continuous classification of animals according to their biomedical need, rather with their evolutionary and ecological significance. This trend is recently prevalent in GigaScience as well as the other journals and reflect an extreme anthropocentric view. I think that the paper will benefit from a statement on how this data contributes to the completeness of the primate research, evolutionary, comparative and conservation studies.

We completely agree with this sentiment and have modified the text to highlight the long-standing importance of baboons as models for non-medical studies (such as evolutionary genetics and animal behavior).