Pooling reads from NovaSeq 6000 and NovaSeq X plus

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Le Qi

• November 02, 2023 15:07

Hi,

I have about 20X coverage-worth of reads from NovaSeq 6000, and I need to sequence them deeper to get 30X. I'm facing the choice of using the NovaSeq 6000 to keep it consistent or using the new NovaSeq X plus that's half the price. Are there any obvious concerns regarding variant calling with DRAGEN-GATK for mixing up reads from different machines? I'm doing this on all my samples, so batch effects will be balanced at least.

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  Gökalp Çelik

  • November 02, 2023 17:51

  Hi Le Qi

  You may consider them as separate libraries for the same sample therefore once LB, RG tags are set properly it really should not be a problem since NovaSeq 6000 and NovaSeq X are not too different from each other in terms of data quality. 

  Regards. 

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  Le Qi

  • November 02, 2023 17:56

  Thank you Gökalp Çelik! 

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