lllumina’s HiSeq 2500 and HiSeq1500: What Can They Sequence?

IlluminaHiSeq-2500-1500The high-throughput sequencing leader Illumina launched HiSeq 2500/1500, as an update from its earlier version of high-throughput sequencer HiSeq 2000/1000, in early this year. Illumina’s HiSeq 2500/1500 expected to be available sometime in the summer 2012.

And this post is part of a series of posts looking at the Next-generation or Second generation high throughput sequencers and ask simple questions on their sequencing capabilities. Here we ask How much do they cost? What can Illumina HiSeq 2500/1500 can do? How much sequence/data HiSeq 2500/1500 produce?

The list price of HiSeq 2500 is $740,000 and the price of HiSeq 1500 is $690,000. These prices are just the prices of the sequencers without including any other accessories.

Illumina HiSeq 2500/1500: Run Modes for Large and Small Data

The HiSeq 2500/1500 are two high-throughput sequencing systems with different capabilities. One of the biggest problems with Illumina machines till recently was that they are suitable for big projects that sequences multiple samples and produce a lot of data, but not good mid-scale experiments. For example, at any given run using Illumina’s 8 lanes in flow cell one has to have enough sample to use the all 8 lanes.

Typical research labs tend to have the need for smaller sequencing projects and can not fill a flow cell. And they are forced to wait until there is enough samples to fill the lanes. If you are outsourcing your sequencing experiments and feel it is taking more time than needed, this might be the issue that is holding your samples from sequencing.

Illumina offers a solution to this problem with HiSeq 2500 and HiSeq 1500 – Illumina’s latest systems which come with two sequencing run modes; one for huge amount of data and the other for producing data rapidly. Illumina calls these run modes as High output and rapid run. In high output mode one can batch multiple samples in a single run to produce high output sequence data. In rapid run mode, Illumina HiSeq 2500/1500 can run fewer samples and produce data fast. As with earlier HiSeq versions, HiSeq 2500 can produce more data compared to HiSeq 1500.

Let us see some numbers or stats on what can HiSeq 1500 do.

HiSeq 1500 Rapid Run Mode: 60 Gb of 100 bp reads in just about a day.

In the rapid run mode HiSeq 1500 can produce 60 Gb of data in 100 bp paired reads in just 27 hours. In each run, HiSeq 1500 can produce 600 Million paired-end reads or 300 Million single reads. The maximum read length HiSeq 1500 can produce is 150 bp in rapid run mode. One of the factors that helps speed up the sequencing process is the cluster generation is done on board in HiSeq 1500 rapid run mode.

HiSeq 1500 High Output Mode: 300 Gb of 100 bp reads in just about a week.

In high output mode, HiSeq 1500 can produce 300 Gb of data in about 8.5 days. In each run, HiSeq 1500 can produce 3 Billion paired-end reads and 1.5 Billion single reads. The maximum read length HiSeq 1500 can produce in high output mode is 100bp. Illumina’s 150 cycle runs to produce 150 bp read is supported only in rapid run mode.

HiSeq 2500 Rapid Run Mode: 120 Gb in 27 hours

To simply put, HiSeq 2500 is HiSeq 1500 on steroid. In rapid run mode, HiSeq 2500 can produces 120 Gb of data, double the size of what HiSeq 1500 can produce in rapid run mode, in the same 27 hours. In each run, HiSeq 2500 produces 1.2 Billion paired-end reads or 600 Million single end reads. Again this double the number of what can HiSeq 1500 can produce in rapid run mode. In the rapid run mode, HiSeq 2500 can sequence of read lengths 150 bp.

HiSeq 2500 High Output Mode: 600 Gb or 6 Billion PE reads in 11 days

The HiSeq 2500 high output mode is suitable for sequencing multiple samples by multiplexing with unique bar codes. In the high output mode, HiSeq 2500 can produce 600 Gb of data, again twice the amount of data as HiSeq 1500 in high output mode but with just an additional 2.5 days. In each high output mode run, HiSeq 2500 produces 6 Billion paired-end reads or 3 Billion single end reads.

The Fastest HiSeq

Comparing the HiSeq 2500 and HiSeq 1500 in all four modes, HiSeq 2500 in the rapid mode is the fastest. In an hour, HiSeq 2500 in rapid mode can sequence 4.44Gb of data (44.44 M reads per hours), while HiSeq 2500 in high output mode produces 2.27 Gb of data in an hour (22.72 M reads per hour), HiSeq 1500 in rapid run mode can produce 2.22 Gb per hour (22.22 M reads per hour), and HiSeq 1500 in high output mode can produce 1.47 Gb per hour (14.7 M reads per hour). HiSeq 2500 rapid run mode wins the race to be the fastest among the two machines running in two different modes.


  1. HiSeq 2500 High Output Mode: 600 Gb or 6 Billion PE reads in 11 hours?? I believe is should be 11 DAYS

  2. nextgenseek says:

    thanks for catching that.

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