CD-HIT identity %

[YJ Kim]

Hi Jim, 

May I ask you how to specify the percentage of identity using CD-HIT when generating markers using 'shortbred_identify command'? 

I would like to use 100% as used in this paper (https://www.nature.com/articles/nature17672).

Best wishes,

Younjung

[Jim Kaminski]

Hi Younjung,

You can obtain 100% id with cd-hit by using these parameter settings: --clustid 1.0 --qclustid 1.0 

"--clustid" sets the clustering identity used by cd-hit in the initial clustering of your input sequences. "--qclustid" sets the clustering identity for quasi markers (if they exist).

Best,

Jim

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