Impact of MEGAHIT Parameter on COBRA Extension?

[shujieH]

Hi Linxing，

I hope you're doing well.

I am working on identifying huge phages from metagenomes. During assembly, I used the parameter --min-contig-len 500 with MEGAHIT, instead of the default settings. I am wondering if this setting could have any impact on the use of the COBRA extension.

Best regards,
Shujie

[linxingchen]

Hi Shujie, That's a good question. I do not suggest you using cobra given that the short contigs have been excluded, two reasons, first is cobra relies on these short ones heavily for joining longer ones, second, there will be risks to extend as cobra could not get the true breaking points without the short ones. I hope this helps. LinXing Chen, Ph.D Special Researcher University of Science and Technology of China Anhui, China shujieH ***@***.***>于2024年12月23日 周一18:10写道：

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Hi Linxing， I hope you're doing well. I am working on identifying huge phages from metagenomes. During assembly, I used the parameter *--min-contig-len 500* with MEGAHIT, instead of the default settings. I am wondering if this setting could have any impact on the use of the COBRA extension. Best regards, Shujie — Reply to this email directly, view it on GitHub <#50>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ALEPRGK2OLXA7MLTMFKABED2G7OR5AVCNFSM6AAAAABUCZCR56VHI2DSMVQWIX3LMV43ASLTON2WKOZSG42TKNRYGQ3TMNA> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[shujieH]

Thank you very much for your timely response, your reply was very helpful!

Best,
Shujie