Reviewer name and names of any other individual's who aided in reviewer	Ryan Wick
Do you understand and agree to our policy of having open and named reviews, and having your review included with the published manuscript. (If no, please inform the editor that you cannot review this manuscript.)	Yes
Is the language of sufficient quality?	Yes
Please add additional comments on language quality to clarify if needed
Is there a clear statement of need explaining what problems the software is designed to solve and who the target audience is?	Yes
Additional Comments	n/a
Is the source code available, and has an appropriate Open Source Initiative license <a href="https://opensource.org/licenses" target="_blank">(https://opensource.org/licenses)</a> been assigned to the code?	Yes
Additional Comments	n/a
As Open Source Software are there guidelines on how to contribute, report issues or seek support on the code?	Yes
Additional Comments	n/a
Is the code executable?	Yes
Additional Comments	n/a
Is installation/deployment sufficiently outlined in the paper and documentation, and does it proceed as outlined?	Yes
Additional Comments	n/a
Is the documentation provided clear and user friendly?	Yes
Additional Comments	n/a
Is there enough clear information in the documentation to install, run and test this tool, including information on where to seek help if required?	Yes
Additional Comments	n/a
Is there a clearly-stated list of dependencies, and is the core functionality of the software documented to a satisfactory level?	Yes
Additional Comments	n/a
Have any claims of performance been sufficiently tested and compared to other commonly-used packages?	Yes
Additional Comments	n/a
Is test data available, either included with the submission or openly available via cited third party sources (e.g. accession numbers, data DOIs)?	Yes
Additional Comments	n/a
Are there (ideally real world) examples demonstrating use of the software?	Yes
Additional Comments	n/a
Is automated testing used or are there manual steps described so that the functionality of the software can be verified?	Yes
Additional Comments	n/a
Any Additional Overall Comments to the Author	This paper was initially submitted as a Technical Release article, but it has since been changed to a Data Release article. The ReView site still lists the article as a Technical Release, and so the specific questions do not apply. As discussed with the editor, I have therefore put ‘n/a’ for each of the fields, and my entire review is here in the ‘Additional Overall Comments to the Author’ section. This manuscript introduces CycloneSEQ data as a means for producing complete bacterial genome assemblies, with a focus on hybrid assemblies made using a combination of CycloneSEQ data and DNBSEQ data. It also publicly provides deep CycloneSEQ+DNBSEQ read sets for a range of bacterial species. Major comments The reads for the project were made publicly available via CNGBdb (https://db.cngb.org/search/project/CNP0006129), but I found it to be unusably slow (both the HTTP website and the FTP data downloads). To ensure the data is accessible to a wide audience, I request that it also be hosted in another location to make it available to readers. For example, SRA, ENA or GigaDB. The paper makes no mention of the other major long-read platforms: Oxford Nanopore Technologies and Pacific Biosciences. Given the widespread use of these platforms (especially ONT) in bacterial genome assembly, some discussion on CycloneSEQ’s relative advantages or limitations would be beneficial. Minor comments Lines 100-103: this sentence (‘The GC content was sensitively affected…’) is not clear to me. How are the completeness and accuracy of the assembly affecting GC content? Figure S2 unnecessarily includes reference-vs-reference difference counts, which are by definition zero. Figure S2 could mention the genome (Akkermansia muciniphila ATCC BAA-835) in the caption – I did not immediately understand what 'for type strain' meant. I found Figure 5 difficult to read, with its use of colour to indicate accuracy. This data would be better shown using another visualisation (e.g. bar plot) that more clearly shows quantitative values. For the mixed microbial community analysis, it should be stated that Unicycler is exclusively designed for bacterial isolates (its documentation explicitly says to not use it on metagenomes). Some of the supplementary figures are erroneously labelled 'Supplementary Table'. Some stats on the metagenomic reads would be helpful: e.g. total bp for short and long reads, N50 for long reads, etc. The methods describe using seqtk, but the reference for this (#25) is SeqKit (a different tool), so either the tool in the methods or the reference is wrong.
Recommendation	Major Revisions