MGI DNBSEQ-T7 DNA Sequencer (Nebula) ….Is it Compatible with GATK Best Practice Pipeline?

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Adi Abuali

• March 22, 2021 17:32

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How do I apply MGI DNBSEQ-T7 DNA Sequencer (Nebula) output to GATK Best Practice pipeline?

Am asking since all best practice documentation is based on illumine (adapters, quality score algorithm, …etc.)

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  Genevieve Brandt (she/her)

  • March 25, 2021 16:17

  Hi Adi Abuali,

  Could you provide more information about the similarities and differences between the sequencing you have and Illumina sequencing? I am not familiar enough with the data you have to make good recommendations at this point.

  Please see this document for what you should include in your post: https://gatk.broadinstitute.org/hc/en-us/articles/360053845952-Forum-Guidelines#write_a_new_post

  Thank you!

  Genevieve

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  SkyWarrior

  • April 02, 2021 16:18

  Completely compatible. Use ILLUMINA as platform tag in sam file. Picard or GATK does not accept MGI as platform name. General base quality and call metrics are very compatible with earlier ILLUMINA devices such as HiSeq 2000 2500. T7 might have adopted something similar to Novaseq but I am not sure. I can talk for DNB-SEQ G400 AKA MGISEQ-2000 and the experience has been quite familiar. 

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  Adi Abuali

  • April 02, 2021 23:08

  Thank you SkyWarrior...

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