NextSeq 1000/2000 Compatible Products

Operating System Compatibility

The following table details the compatibility relationship between operating system, control software version, and sequencing chemistry type.

Operating System Control Software Version Sequencing Chemistry
Oracle Linux 9 2.0 and higher XLEAP-SBS chemistry
CentOS 7 1.7 and lower XLEAP-SBS chemistry and Standard SBS chemistry

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 2.0  
4.2.11 Not available Not available
  • Amplicon
  • BCL Convert
  • Enrichment
  • Germline
  • RNA
  • Single Cell RNA
4.2.9 Not available
  • BCL Convert
  • Germline
  • RNA
Not available
4.2.7 Not available
  • Amplicon (DNA)
  • BCL Convert
  • Enrichment
  • Germline
  • RNA
  • Sincle Cell RNA
Not available
3.10.12
  • Amplicon (DNA)
  • BCL Convert
  • Enrichment
  • Germline
  • RNA
  • Single Cell RNA
Not available Not available
3.9.3
  • BCL Convert
Not available Not available
3.8.4
  • Amplicon (DNA)
  • BCL Convert
  • Enrichment
  • Germline
  • RNA
  • Single Cell RNA
Not available Not available
3.7.4
  • BCL Convert
  • Enrichment
  • Germline
  • RNA
  • Single Cell RNA
Not available Not available
3.5.8 Not available Not available Not available
3.5.6 Not available 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.