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 |
|
|
| 3.10.12 |
|
Not available | |
| 3.9.3 |
|
Not available | |
| 3.8.4 |
|
Not available | |
| 3.7.4 |
|
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.