Circularization undocumented

[lskatz]

Could you document circularization? I see in the source code that there is some kind of logic where SKESA will add _Circ to a defline but it is unclear what those conditions are. Or even more importantly, could you add to the documentation that _Circ indicates circularization and list any caveats? Thank you!

I see it around here but it is otherwise not mentioned in the repo.

https://github.com/ncbi/SKESA/blob/v2.3.0/skesa.cpp#L150

[souvorov]

Please check two last paragraphs of Multi-threading chapter of the original SKESA paper (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6172800/).

From: Lee Katz @.> Sent: Thursday, November 17, 2022 2:44 PM To: ncbi/SKESA @.> Cc: Subscribed @.***> Subject: [EXTERNAL] [ncbi/SKESA] Circularization undocumented (Issue #35)

Could you document circularization? I see in the source code that there is some kind of logic where SKESA will add _Circ to a defline but it is unclear what those conditions are. Or even more importantly, could you add to the documentation that _Circ indicates circularization and list any caveats? Thank you!

I see it around here but it is otherwise not mentioned in the repo.

https://github.com/ncbi/SKESA/blob/v2.3.0/skesa.cpp#L150https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fncbi%2FSKESA%2Fblob%2Fv2.3.0%2Fskesa.cpp%23L150&data=05%7C01%7Csouvorov%40ncbi.nlm.nih.gov%7Ceea2830e20a74d5d7b4408dac8d415c5%7C14b77578977342d58507251ca2dc2b06%7C0%7C0%7C638043110468125134%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=ByS4f%2BqjF%2B09nVezeoAz1qfw0lFEXzmqMGlhV36%2F%2BAI%3D&reserved=0

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[lskatz]

Ah thanks for noting it there and pointing me in the right direction! I feel like you're saying that the documentation for SKESA therefore lives in the publication? Is that correct?

[souvorov]

I'm glad it was helpful. Yes, the publication describes the method used in much more details.

From: Lee Katz @.> Sent: Friday, November 18, 2022 10:41 AM To: ncbi/SKESA @.> Cc: Souvorov, Alexander (NIH/NLM/NCBI) [E] @.>; Comment @.> Subject: [EXTERNAL] Re: [ncbi/SKESA] Circularization undocumented (Issue #35)

Ah thanks for noting it there and pointing me in the right direction! I feel like you're saying that the documentation for SKESA therefore lives in the publication? Is that correct?

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