NextSeq 500 Illumina

Room: 609

Contact: Katarzyna Misztal

Access: Operator only

Next Seq 500

General Description

NextSeq 500 Illumina is a benchtop and lab-scale Sequencer from Illumina. It works in two configurations High and Mid Output and can sequence up to 400 M single reads of maximal length 300 bp. BaseSpace onsite Server is used for automated base calling and Fastq files generation.


NextSeq 500 Performance parameters

Flow cell configuration

Read length


Run time

High Output (up to 400 M single reads)

2 x 150 bp

2 x 75 bp

1 x 75 bp

100-120 Gb

50-60 Gb

25-30 Gb

29 h

18 h

11 h

Mid Output (up to 130 M single reads)

2 x 150 bp

2 x 75 bp

32-39 Gb

16-19 Gb

26 h

15 h

Key Applications

  • Transcriptome Sequencing (total RNA-Seq, mRNA-Seq, gene expression profiling)
  • DNA-Protein Interaction Analysis (ChIP-seq)
  • Small Whole-Genome Sequencing (microbe, virus)
  • Targeted Gene Sequencing (amplicon-based, gene panel)
  • Exome Sequencing

Sample Preparation

ü                   RNA and DNA isolation

ü                Library preparation

  • DNA or RNA library can be prepared with home-made or commercially available kits offered by many companies compatible with Illumina technology. (link: protocols in NGS lab).

Further reading

  1. Intro_NextSeq_System_manual
  2. Illumina Adapter Sequences
  3. Index Adapters Pooling Guide
  4. ENCODE sequencing recommendations