Illumina HiSeq 2500

The Illumina HiSeq 2500 has been replaced by the Illumina NextSeq, Illumina has designated the HiSeq 2500 as obsolescent and all support of the instrument will be ending. HiSeq 2500 is only available for applications that can’t be performed on the NextSeq (e.g. 250 x 250 paired-end sequencing). 


  • Two flow cells.
  • Eight-lane High-Output mode and two-lane Rapid-Run mode available.
  • Up to 1.5 billion single reads (or 1.5 billion pairs of reads) per High-Output flow cell.
  • Up to 300 million single reads (or 300 million pairs of reads) per Rapid-Run flow cell.
  • Single read sequencing up to 100 nt in High-Output and 250 nt in Rapid-Run mode.
  • Paired-end sequencing up to 100 x 100 nt in High-Output and 250 x 250 in Rapid-Run mode.
  • Sample multiplexing available up to 96-384, depending on the application.


The sequencing chemistry is similar across all Illumina platforms. Libraries compatible with one Illumina sequencer should be compatible with all Illumina sequencers.

Used for a variety of applications, including but not limited to:

  • De novo whole genome sequencing
  • Whole genome resequencing
  • Exome sequencing
  • mRNA-Seq
  • miRNA/small RNA-Seq
  • ChIP-Seq
  • RIP-Seq
  • Degradome sequencing

Data is produced in the FASTQ format. This instrument is operated by Genomics Core Facility staff in conjunction with next-generation sequencing services.