NextSeq 1000/2000 Compatible Products
NextSeq 1000/2000 Sequencing System
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.
Reference Genomes
On-instrument Reference Genomes
| Genome Name | Display Name | Species | GTF Available |
|---|---|---|---|
| hg19_alt_aware | Human UCSC hg19 Custom Alt Aware | Homo sapiens [Human] | Yes |
| hg19_no_alt_haps_no_decoys | Human UCSC hg19 Custom Alt Aware No Alt Haps No Decoys | Homo sapiens [Human] | Yes |
| hs37d5 | Human NCBI hs37d5 | Homo sapiens [Human] | Yes |
| hg38_alt_aware | Human 1000 Genomes hg38 Alt Aware | Homo sapiens [Human] | Yes |
| hg38-noalt-with-decoy | Human 1000 Genomes hg38 Noalt with Decoys | Homo sapiens [Human] | Yes |
| mm10 | Mouse mm10 | Mus Musculus [House Mouse] | Yes |
| phix | Phix | PhiX | No |
| rn6 | Rat rn6 | Rattus Norvegicus [Norway Rat] | Yes |
| Rhodobacter_sphaeroides_2.4.1 | R.Sphaeroides 2.4.1 | Rhodobacter Sphaeroides [Bacterium] | No |
| Bacillus_cereus_ATCC_10987 | B.cereus ATCC_10987 | Bacillus Cereus [Bacterium] | No |
| WBcel235 | C.elegans Ensembl WBcel235 | Caenorhabditis Elegans [Roundworm] | No |
| A_Thaliana | A.Thaliana | Arabidopsis Thaliana | No |
| eschColi_K12_1 | E.Coli Strain K12 | Escherichia Coli [Strain K12] | No |
Reference Genome Recommendations
If using DRAGEN BIO-IT Platform for secondary analysis, the following are the recommended reference genomes for each pipeline.
Illumina Germline Pipeline and Illumina Enrichment Pipeline
- 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
- 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.