How Does a Single HiSeq X Compares With HiSeq 2500?

Illumina HiSeq X v HiSeq 2500

Illumina HiSeq X v HiSeq 2500

Illumina launched its most powerful sequencing system, HiSeq X Ten at today’s JPM 2014. Illumina HiSeq X  Ten is a set of 10 HiSeq X machines that will Illumina will sell together for population based sequencing projects.  With HiSeq X Ten Illumina breaks the $1000 genome barrier for the first time.

A single HiSeq X machine can produce 1.8Tb of data in three days, i.e about 600 Gb of data per day. When running 10 machines of HiSeq X in parallel, the data output just blows up and one can sequence more than 18,000 genomes at 30X coverage in a year.

A single HiSeq X can be run with either a Single Flow Cell or Dual Flow Cell and they both support paired end reads of length 2x 150 bp. In less than three days, Dual Flow Cell can produce 1.6-1.8Tb data per run (6 billion SE reads) and the Single Flow Cell can produce 800-900Gb per run (3 billion SE reads).

So how does HiSeq X compares to the existing HiSeq 2500?  Both HiSeq X and HiSeq 2500 have Single and Dual Flow Cells. However, HiSeq X does not have the Rapid Run mode/High Output Mode options. The Rapid/High output modes are shunted to Illumina NextSeq 500 and HiSeq X is all about raw power to produce more data fast.

The maximum amount of data from HiSeq 2500 is produced in High Output mode, producing 900 Gb to 1Tb of data in Dual Flow Cell with 2 x 125 bp reads. And this run would take 6 days to finish. On the other hand, a single HiSeq X using Dual Flow Cell can produce 1.6-1.8Tb data per run in less than three days.

Naively, a single HiSeq X is almost four times faster with  

  • HiSeq 2500 producing 1TB in six days
  • HiSeq X producing 3.6Tb in six days

For comparison of NextSeq 500 to MiSeq and HiSeq, visit

 To get a first look at the Illumina Sequencer Family: HiSeq X and NextSeq 500, check







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