NextSeq 1000/2000 FAQs

  • Analysis


  • The options are based on the available DRAGEN pipelines:

    • [DRAGENEnrichment_Settings] and [DRAGENEnrichment_data]
    • [DRAGENGermline_Settings] and [DRAGENGermline_data]
    • [DRAGENRNA_Settings] and [DRAGENRNA_data]
    • [DragenSingleCellRNA_Settings] and [DragenSingleCellRNA_data]
    • Cloud mode—Plan your run with Instrument Run Setup on BaseSpace Sequence Hub. The run is selected from a list of planned runs in NextSeq 1000/2000 Control Software. During sequencing, cBCL data are uploaded to BaseSpace Sequence Hub. The selected analysis workflow is initiated automatically within the cloud. Run data and analysis results are also provided in the cloud.
    • Hybrid mode—Plan your run with Instrument Run Setup on BaseSpace Sequence Hub. The run is selected from a list of planned runs in NextSeq 1000/2000 Control Software. The selected analysis workflow is then initiated through the on-instrument DRAGEN.
    • Local mode—Plan your run with a sample sheet v2 file format locally. The selected analysis workflow is initiated automatically through the on-instrument DRAGEN or manually through BaseSpace Sequence Hub apps after run completion when Proactive, Run Monitoring and Storage is selected.
    • Standalone mode—Plan your run without a sample sheet, following the instructions in NextSeq 1000/2000 Control Software to generate cBCL data.

    Analysis is available through the on-board DRAGEN Bio-IT Platform or on the cloud using BaseSpace Sequence Hub. The following DRAGEN pipelines are available:

    • DRAGEN BCL Convert
    • DRAGEN Enrichment
    • DRAGEN Germline
    • DRAGEN RNA
    • DRAGEN Single Cell RNA
  • Reagents


  • Custom primers are supported for the NextSeq 1000/2000 P1 Reagents kit, the NextSeq 1000/2000 P2 Reagents kit, and the NextSeq 2000 P3 Reagents kit. If using the NextSeq 1000/2000 P2 (v2) Reagents kit (catalog # 20043738, 20043737, and 20043736), you will need to use a custom recipe to use custom primers. See Product Files for more information. 

    Yes, the reagents kits for the NextSeq 1000/2000 Systems include all consumables to support both single-read and paired-end sequencing. During run setup, you can configure the run to generate either single-read or paired-end data.