The NextSeq 500 can be run in either high- or mid-output modes:

Run parameters 

  • Up to 130 million reads (260 million paired end) per mid-output run
  • Up to 400 million reads (800 million paired end) per high-output run
  • Single-read or paired-end
  • Read lengths of 75 or 150 bp
  • Total output up to 39 Gb (mid output) or 120 Gb (high output) per run. Run durations up to 29 hours. 


Applications include:

  • Genomic DNA sequencing
  • Exome sequencing
  • mRNA sequencing
  • smallRNA/microRNA sequencing
  • Epigenetics
    • Chromatin immunoprecipitation sequencing
    • DNA methylation
  • Small genome DNA sequencing (de novo & resequencing)
  • Targeted resequencing, such as gene panels

At the moment, Illumina has not approved the use of the NextSeq 500 for low diversity libraries (typical of amplicon sequencing) or for libraries with inserts longer than 500 bp.



The NextSeq offers faster turnaround time (shorter run time and no need to fill an entire flow-cell of 8 lanes, as needed on the Hiseq-platform, so no waiting for other users´samples). It is ideal for small-medium sized high priority Projects.

Published Oct. 27, 2016 12:14 PM - Last modified Oct. 27, 2016 1:16 PM