Illumina HiSeq

The HiSeq range is the flagship of the Illumina high-throughput sequencing platforms and come in many flavours 2500, 3000, 4000 and X. At the Earlham Institute we have a mix of platforms, the 2500 and 4000 machines. These use Illumina’s sequencing-by-synthesis chemistry, although there are differences between the platforms.

The 3000, 4000 and X have ‘patterned’ flowcells which allow higher throughput. The 2500 does not have patterned flowcells, but is capable of producing reads of up to 250 bases. The 3000, 4000 and X can produce reads of 150 bases. The X is limited to only genome sequencing and is not licenced for use on all genomes.

Find out about the differences between the 1500 and 2500 as well as the 3000 and 4000 systems.

Illumina HiSeq

The applications.

Everything! These are our workhorse machines for RNA-Seq, genome sequencing, resequencing and exome sequencing. We are able to massively multiplex samples, up to about 10,000 per lane.

The throughput.

Our 2500 machines run in 2 modes, ‘High Output’ and ‘Rapid Run’. In High Output mode, the machines are capable of producing 1 Tb of sequence data (8 billion, 125 base, paired-end reads) per run.

Our 4000 machines only run in one ‘High Output’ mode, and can generate 1.5Tb of data (10 billion, 150 base, paired-end reads) per run.

What we use it for.

The HiSeqs power all of our high throughput genomics work whether that is BAC library sequencing, exome capture of thousands of crop lines, sequencing the genomes of ferrets, koalas and fish or untangling the wheat transcriptome via RNA-Seq. The 2500 is a particularly important part of our capacity. Despite being a slightly older machine, we use the long reads of the Rapid Run mode (250 base, paired-end reads) which are able to be used to generate very high quality genome assemblies when paired with the right assembly software, and some long-mate pair data.

Related reading.