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Cambridge Genomic Services

A Next-Generation Sequencing and Array Facility in the Department of Pathology

Studying at Cambridge


Sequencing Run

MiSeq with scientistCGS has two instruments available in house, the NexSeq500 and the MiSeq but also we can have access to a HiSeq 4000.

To decide on the best instrument and run type there are several factors to take in to account:

  • The application: depending on the application and therefore the library preparation and the library fragment size, the most appropriate read length and single-end or paired-end sequencing will be important decisions to make.


  • The amount of data to sequence: that would be the size of the genome or transcriptome to sequence. This is useful information to know particularly if working on non-model organisms or on custom libraries such as amplicon or targeted libraries. This information is essential to determine which instrument will be best suited.


  • Coverage/resolution: this will depend on the application and objective. There are general recommendations on the various applications as well as publications for references.


  • Project size: depending on the number of samples and all the above a final decision can be made on the instrument and run type and number of runs/lanes necessary.


  • Budget/time constraints: They are important consideration for most researchers. The price per base sequenced increases as the instrument output diminishes. So a HiSeq4000 for instance is more attractive financially. However it is not always the best choice. Having access to a Hiseq is generally more difficult with longer turn around time or inadequate output for the project. If working on large genomes, or large projects with a need of several lanes, the Hiseq4000 is the obvious choice as the instrument can be run with 8 or 16 lanes. For smaller project on the other hand when someone would need 1-3 runs, the NextSeq and MiSeq become attractive because it is one lane only and enables a rapid turn-around and the run type/output can be exactly tailored to the needs of the individual projects thus maximising a run and delivering the adequate coverage or resolution at the right price.

We will guide you with all of the above so you can make an informed decision on the most appropriate sequencing approach for your project.

NGS Application Table.jpg

NextSeq spec table

MiSeq spec table