Next Generation Sequencing

Edinburgh Genomics delivers high-throughput, next generation sequencing data from Illumina, Pacific Biosciences, and Oxford Nanopore systems.

The facility operates Illumina MiSeq and NovaSeq systems, as well as the PacBio Sequel, and the Oxford Nanopore PromethION and thus has the largest capacity of any University-based sequencing facility in the UK.

The NovaSeq, Sequel and PromethION are capable of generating many tens of gigabases per day. These data can be...

  •     assembled de novo to predict the sequence of a new genome or transcriptome
  •     aligned to a reference genome to identify single nucleotide or insertion-deletion polymorphisms
  •     used to count the abundance of species in a DNA mix. The mixes can be the 3' ends of transcripts, small RNAs such as microRNAs or DNA fragments generated by chromatin immunoprecipitation (ChIP) experiments.

We can multiplex many samples per run, so whether you want a "small" number of short reads or hundreds of gigabases, we can deliver.


 

Applications

Our sequencing instrumentation is very versatile: if the sample is nucleic acid, we can transform it to a sequencable library. Data generated by Edinburgh Genomics have been applied to questions in a wide range of fields:

 | Genome assembly | SNP discovery | CNV mapping | Genome rearrangements | Genome architecture | Epigenetic modification | Genetic mapping | Quantitative trait genetics | Population genetics | Metagenomics | Metagenetics | Mutation screening | Synthetic biology | Transcriptome assembly | Gene expression | Transcriptional regulation | Phenotyping of mutants | Pathogen discovery | Evolutionary genomics | Host-pathogen interaction | Ecotoxicogenomics |

The Illumina MiSeq and NovaSeq instruments are suited to a wide range of approaches, including:

DNA-Seq:

  •     De novo genome sequencing
  •     Genome resequencing
  •     Targeted resequencing
  •     Exome sequencing
  •     Amplicon sequencing
  •     ChIP sequencing (and variants, including 5C)
  •     Methylome sequencing
  •     Genotyping by sequencing
  •     Reduced representation sequencing
  •     Restriction site associated DNA (RAD) sequencing

RNA-Seq:

  •     De novo transcriptome sequencing
  •     Digital transcriptomics
  •     Small RNA sequencing
  •     Total RNA sequencing
  •     Expressed sequence RAD
  •     Stranded RNA sequencing

Technologies

Illumina NovaSeq and MiSeq

Illumina sequencing produces data at rates orders of magnitude faster than Sanger sequencing, but generates shorter sequences (50 to 300 bases each). Millions to billions of DNA molecules are covalently attached to the surface of a treated glass flowcell, and each individual molecule is amplified in situ to generate a "cluster" that contains about 1000 copies. Sequences are read from newly synthesised DNA copied from these targets by incorporation of fluorescently-tagged nucleotide analogues, illumination with a laser and optical capture of signal from all the amplified clusters simultaneously.

The instruments installed in Edinburgh Genomics are the MiSeq and NovaSeq.

PacBio Sequel

The PacBio Sequel is based on the RSII proven single molecule, real-time technology with the potential deliver around 7x more reads per SMRT cell.  This platform delivers long reads, high consensus accuracy, uniform coverage and epigenetic characterisation and is ideal for generating high-quality whole genome de novo assemblies. Edinburgh Genomics is proud to be one of the first facilities in the UK to be able to offer this new technology to the sequencing community. Contact us to take advantage of this exciting new long-read technology for applications including De novo genome assemblies, structural variation, full length transcripts, long amplicons and real time methylome detection.

Oxford Nanopopre PromethION

The ONT PromethION offers real-time, long-read, direct DNA and RNA sequencing technology at a large scale.  It offers the same pore-based sequencing as the MinION, but with many more pores for a much higher throughput and lowe cost per base.