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.

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.