NextSeq 1000/2000 Compatible Products

Sample Information

Choose from the following options to record information about your samples, such as sample ID and which index adapters are used for pooling. 

  • If using cloud or hybrid mode, use the Instrument Run Setup in BaseSpace Sequence Hub. 
  • If using local mode, use a Sample Sheet v2 template

Data Analysis

Use Sequencing Analysis Viewer or BaseSpace Sequence Hub to monitor real-time quality metrics during a run.

To analyze sequencing data, choose from the following options:

The NextSeq 1000/2000 Sequencing System performs secondary analysis using the on-intsrument DRAGEN BIO-IT Platform. See the NextSeq 1000/2000 Sequencing System Guide for more information.

Single Cell RNA Product Compatibility

The DRAGEN Single Cell RNA analysis pipeline provides compatibility with third-party kits. For more information on third-party kit compatibility, see Single Cell RNA Product Compatibility.

DRAGEN Workflow Version Compatibility

The following DRAGEN workflow versions are compatible with the NextSeq 1000/2000 Control Software versions.


  Control Software Version  
DRAGEN Version 1.2 - 1.5 1.7  
4.2.7 Not available
  • Amplicon (DNA)
  • BCL Convert
  • Enrichment
  • Germline
  • RNA
  • Sincle Cell RNA
3.10.12
  • Amplicon (DNA)
  • BCL Convert
  • Enrichment
  • Germline
  • RNA
  • Single Cell RNA
Not available
3.9.3
  • BCL Convert
Not available
3.8.4
  • Amplicon (DNA)
  • BCL Convert
  • Enrichment
  • Germline
  • RNA
  • Single Cell RNA
Not available
3.7.4
  • BCL Convert
  • Enrichment
  • Germline
  • RNA
  • Single Cell RNA
Not available
3.5.8 Not available Not available
3.5.6 Not available Not available

Reference Genomes

On-instrument Reference Genomes
Genome Name Display Name Species GTF Available DRAGEN Versions
hg19_alt_aware Human UCSC hg19 Custom Alt Aware Homo sapiens [Human] Yes 3.5, 3.7, 3.8, 3.10
hg19_no_alt_haps_no_decoys Human UCSC hg19 Custom Alt Aware No Alt Haps No Decoys Homo sapiens [Human] Yes 3.5, 3.7, 3.8, 3.10
hg19_alt_aware_graph_based Human UCSC hg19 Custom Alt Aware Graph Homo sapiens [Human] Yes 3.8, 3.10
hg19-alt-masked_v3 Homo sapiens [UCSC] hg19 Alt Masked v3 Homo sapiens [Human] Yes 4.2
hg19-alt-masked.graph_v3 Homo sapiens [UCSC] hg19 Alt Masked v3 Graph Homo sapiens [Human] Yes 4.2
hs37d5 Human NCBI hs37d5 Homo sapiens [Human] Yes 3.5, 3.7, 3.8, 3.10
hs37d5_graph_based Human NCBI hs37d5 Graph Homo sapiens [Human] Yes 3.8, 3.10
hs37d5_v3 Homo sapiens [NCBI] hs37d5 v3 Homo sapiens [Human] Yes 4.2
hs37d5.graph_v3 Homo sapiens [NCBI] hs37d5 v3 Graph Homo sapiens [Human] Yes 4.2
hg38_alt_aware Human 1000 Genomes hg38 Alt Aware Homo sapiens [Human] Yes 3.5, 3.7, 3.8, 3.10
hg38-noalt-with-decoy Human 1000 Genomes hg38 Noalt with Decoys Homo sapiens [Human] Yes 3.5, 3.7, 3.8, 3.10
hg38_alt_aware_graph_based Human 1000 Genomes hg38 Alt Aware Homo sapiens [Human] Yes 3.8, 3.10
hg38-alt-masked_v3 Homo sapiens [1000 Genomes] hg38 Alt Masked v3 Homo sapiens [Human] Yes 4.2
hg38-alt-masked.graph_v3 Homo sapiens [1000 Genomes] hg38 Alt Masked v3 Graph Homo sapiens [Human] Yes 4.2
mm10 Mus musculus [UCSC] mm10 Mus Musculus [House Mouse] Yes 3.5, 3.7, 3.8, 3.10, 4.2
phix Microvirus Escherichia virus phiX174 [NCBI] PhiX No 3.5, 3.7, 3.8, 3.10, 4.2
rn6 Rattus norvegicus [UCSC] rn6 Rattus Norvegicus [Norway Rat] Yes 3.5, 3.7, 3.8, 3.10, 4.2
Rhodobacter_sphaeroides_2.4.1 R.sphaeroides [NCBI] 2.4.1 Rhodobacter Sphaeroides [Bacterium] No 3.5, 3.7, 3.8, 3.10, 4.2
Bacillus_cereus_ATCC_10987 B. cereus [NCBI] ATCC_10987 Bacillus Cereus [Bacterium] No 3.5, 3.7, 3.8, 3.10, 4.2
WBcel235 C. elegans [Ensembl] WBcel235 Caenorhabditis Elegans [Roundworm] No 3.5, 3.7, 3.8, 3.10, 4.2
A_Thaliana A. thaliana [TAIR] TAIR10 Arabidopsis Thaliana No 3.5, 3.7, 3.8, 3.10, 4.2
eschColi_K12_1 E. coli [NCBI] K12 MG1655 Escherichia Coli [Strain K12] No 3.5, 3.7, 3.8, 3.10, 4.2
Reference Genome Usage Recommendations

If using DRAGEN BIO-IT Platform for secondary analysis, the following are the recommended reference genomes for each DRAGEN pipeline.

Illumina Germline Pipeline and Illumina Enrichment Pipeline (DRAGEN v3.10 or Below)
  • Use ALT-aware mapping when possible.
  • Use the Homo sapiens [1000 Genomes] hg38 Custom Alt Aware reference genome. 
  • If not using hg38, the Homo sapiens [UCSC] hg19 Custom Alt Aware or Homo sapiens [NCBI] hs37d5 are recommended.
Illumina RNA Pipeline (DRAGEN v3.10 or Below)
  • Use no-ALT when possible. 
  • Use the Homo sapiens [1000 Genomes] hg38 No Alt Haps or Homo sapiens [UCSC] hg19 No Alt Haps reference genome.
  • If hg38  or hg19  are not available, any reference genome is suitable.
Illumina Germline Pipeline, Enrichment Germline Pipeline, and Amplicon Germline Pipeline (DRAGEN v4.2 and Above)
  • Use ALT-Masked mapping.
  • Use Graph genomes.
  • Use the Homo sapiens [1000 Genomes] hg38 Alt Masked Graph v3 reference genome. 
  • If not using hg38, the Homo sapiens [UCSC] hg19 Alt Masked Graph v3 or Homo sapiens [NCBI] hs37d5 v3 Graph are recommended.
  • Non-graph is supported, but has reduced accuracy.
Illumina Enrichment Somatic, Amplicon Somatic, RNA, and scRNA Pipelines (DRAGEN v4.2 and Above)
  • Use ALT-Masked mapping.
  • Use non-Graph genomes.
  • Use the Homo sapiens [1000 Genomes] hg38 Alt Masked v3 reference genome or Homo sapiens [UCSC] hg19 Alt Masked v3 reference genome.