Reviewer name and names of any other individual's who aided in reviewer	Ergude Bao
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
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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
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As Open Source Software are there guidelines on how to contribute, report issues or seek support on the code?	Yes
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Is the code executable?	Yes
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Is installation/deployment sufficiently outlined in the paper and documentation, and does it proceed as outlined?	Yes
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Is the documentation provided clear and user friendly?	Yes
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Is there a clearly-stated list of dependencies, and is the core functionality of the software documented to a satisfactory level?	Yes
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Have any claims of performance been sufficiently tested and compared to other commonly-used packages?	Yes
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Are there (ideally real world) examples demonstrating use of the software?	Yes
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Is automated testing used or are there manual steps described so that the functionality of the software can be verified?	Yes
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Any Additional Overall Comments to the Author	This manuscript introduces SMARTdenovo, a de novo assembler for long noisy reads. The assembler has been published since 2015 widely used in various sequencing projects, and has had positive impacts on many de novo assemblers such as MECAT, Minimap2 and Wtdbg2. This manuscript details the algorithm step by step, including an overlapper wtzmo, a trimmer wtclp, a layout algorithm wtlay and a consensus algorithm wtcns. Novel ideas include homopolymer contracting and repeat weighing strategies. Besides the already published experimental results, this manuscript also exhibits some additional ones on species D. melanogaster and S. pennellii. SMARTdenovo can generate continuous and accurate contigs with small running time. This manuscript is well-written and considering SMARTdenovo’s impact, I do not have any additional comment. Indeed, I have been waiting for the publication of SMARTdenovo for a long time, and it is honorable for me to have this chance of review. Ergude Bao School of Software Engineering Beijing Jiaotong University
Recommendation	Accept