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. 2021 Dec 10;2021:gigabyte35. doi: 10.46471/gigabyte.35
Reviewer name and names of any other individual's who aided in reviewer Walter Wolfsberger
Do you understand and agree to our policy of having open and named reviews, and having your review included with the published papers. (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
Are all data available and do they match the descriptions in the paper? Yes
Additional Comments The data on the FTP server available to me covers everything mentioned in the paper.
Are the data and metadata consistent with relevant minimum information or reporting standards? See GigaDB checklists for examples <a href="http://gigadb.org/site/guide" target="_blank">http://gigadb.org/site/guide</a> Yes
Additional Comments
Is the data acquisition clear, complete and methodologically sound? Yes
Additional Comments
Is there sufficient detail in the methods and data-processing steps to allow reproduction? Yes
Additional Comments
Is there sufficient data validation and statistical analyses of data quality? Yes
Additional Comments
Is the validation suitable for this type of data? Yes
Additional Comments
Is there sufficient information for others to reuse this dataset or integrate it with other data? Yes
Additional Comments 1) The submission body and the table 1 state the following assembly stats of the genome assembly that seem to indicate some potential issues: Genome size (Gb) 3.39 No. scaffolds 1,116 No contigs 3,016 Scaffold N50 (Mb) - 6.94 Contig N50 (Mb)- 1.99 The main issue here for me lies in Scaffold N50 in relation to other parameters, when in comparison with the assemblies using similar methodological approach. This can either be good or bad, as these numbers might indicate an issue during scaffolding, or presence of long top assembly scaffolds (which is great). I believe, that the submission would significantly benefit if this information is mentioned and discussed.
Any Additional Overall Comments to the Author The approach used to generate the assembly seems to utilize 10x PE sequences to scaffold the assembly. There are hybrid assembly approaches available, that leverage short reads to improve the assembly quality, given the slightly limited coverage of PacBio HiFi reads(approx. 12x).
Recommendation Minor Revision