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linxingchen / cobra

A tool to raise the quality of viral genomes assembled from short-read metagenomes via resolving and joining of contigs fragmented during de novo assembly.
MIT License
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Group Extended_partial #39

Open SergeyBaikal opened 2 weeks ago

SergeyBaikal commented 2 weeks ago

Dear developers. Could you clarify please. Why is the group Extended_partial based on checkV results circularized (with DTR)? Can I take these sequences as putative complete genomes?

linxingchen commented 2 weeks ago

Hi,

Thank you for using COBRA.

Generally, if a COBRA "Extended_partial" sequence was recognized as "circularized" by CheckV because of DTR, then usually, the length of DTR is not equal to the maximum kmer size you used. In such cases, I would prefer seeing it as a partial genome, you could assign it as a circular genome as well at your own risk. I hope this helps.

Please let me know if you have any other questions.

Have a good day.

LinXing Chen, Ph.D. Special Researcher (特任研究员), University of Science and Technology of China (USTC), HeiFe, Anhui, China Phone: (+86)176-0730-1276 Email: @.***

Sergey Potapov @.***> 于2024年7月7日周日 10:55写道：

Dear developers. Could you clarify please. Why is the group Extended_partial based on checkV results circularized (with DTR)? Can I take these sequences as putative complete genomes?

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