Genomics facilities

We support all aspects of next-generation sequencing projects, from sample to data

  • Our services include consultation in designing experiments, library preparation, sequencing, analysis and interpretation of sequencing data as well as dissemination of results.
  • Please contact us to arrange fpr a consultation to discuss your project.
  • We welcome research collaborations with our users and projects will be considered on an individual basis upon submission of a detailed project proposal.
  • Our services are available to both internal and external users from the academic and private sectors.

Services

Portfolio

We currently support the following next-generation sequencing applications:

Whole Genome Sequencing Shotgun
Whole Exome Sequencing Exons  |  Exons+UTR  |  Exons+Custom Target (6.8Mb)
Custom Target Capture 1-499kb  |  0.5-2.9Mb  |  6-11.9Mb  |  12-24Mb
Amplicon Sequencing Illumina TruSeq Custom Amplicon
RNA Sequencing mRNA (polyA+) stranded  | total RNA (polyA+/-) stranded with cytoplasmic & mitochondrial rRNA removal  |  Small RNA
Methylation Profiling RRBS-seq  |  Bisulphite-seq
16s Metagenomic Profiling V3/V4 Regions  |  Custom Regions
ChIP Sequencing  
We currently support the following next-generation sequencing applications


We will consider non-established protocols on a collaborative basis. Please contact us to discuss your requirements.

Internal users can find information regarding costs for these services on Pricing (behind login).

Experimental design

We provide support for the experimental design, troubleshooting and optimisation of next-generation sequencing projects. We can assess feasibility and suggest the optimal experimental design for your project, taking into account sample availability and budget constraints. We provide advice on the choice of sample, sample sizes, sample collection and extraction. We provide library preparation and advise on the choice of read length, read type (single vs. paired-end) and sequencing depth.

We encourage our customers to get in touch with us as early as possible, ideally at the planning stage of their project. This allows us to identify any potential problems with the experimental design that could impact on the subsequent bioinformatics analysis, and to help customers achieve their desired outcomes.

Internal users can find information regarding costs for these services on Pricing (behind login).

Library preparation

We provide support on all aspects of sample library preparation and offer a comprehensive service for a wide range of next-generation sequencing applications. The facility has dedicated technical support and up-to-date equipment for sample quality control (QC) and the preparation of DNA/RNA libraries for next-generation sequencing projects. Our equipment includes the Covaris S2 DNA sonication system, Agilent Technologies Bioanalyzer 2100, Life Technologies Qubit fluorometer, and Life Technologies StepOnePlus™ Real-Time PCR System.

Internal users can find information regarding costs for these services on pricing (behind login).

Sequencing

The facility caters for the sequencing needs of both small and large-scale genomics projects providing access to two Illumina sequencing systems, the Illumina HiSeq 2500 and Illumina MiSeq.

The HiSeq 2500 System features two run modes – rapid- and high-output-mode – for one or two flow cells simultaneously, enabling a flexible and scalable platform. Rapid-run mode provides quick results, efficient processing of a limited number of samples, and longer paired-end 150 base pair reads, which allow greater depth of coverage and improved assembly for de novo applications. High-output mode is perfect for larger studies with more samples or when the greatest depth of coverage is required. It generates around 600 Gb or six billion paired-end reads in 11 days.

The Illumina MiSeq is the only personalised sequencing system capable of automatically producing paired-end reads with a very fast run time, ranging from 3.5 hours to 35 hours. The single lane flow cell can accommodate up to 7Gb with 24-30 million paired-end reads per run and integrates amplification, sequencing and data analysis in a single instrument.

We offer the following sequencing modes on the HiSeq and MiSeq systems:

Illumina HiSeq 2500 High Output Mode (TruSeq v3 chemistry, 8 lanes per flowcell)
Read length [bases]Sequenced fragments per lane* [millions]Reads per lane* [millions]Output per lane* [giga bases]Approx. runtime [days]
1 x 50 168 - 187 168 - 187 8.4 - 9.4  2
2 x 50 168 - 187 336 - 374 16.8 - 18.7  5.5
1 x 100 168 - 187 168 - 187 16.8 - 18.7  5
2 x 100 168 - 187 336 - 374 33.6 - 37.4  11
*Based on performance specifications provided by the manufacturer. Output may vary depending on sample quality, cluster density and other experimental factors.
Summary of the table's contents

Illumina HiSeq 2500 Rapid Mode (Rapid v3 chemistry, 2 lanes per flowcell)
Read length [bases]Sequenced fragments per lane* [millions]Reads per lane* [millions]Output per lane* [giga bases]Approx. runtime [hours]
1 x 50 125 - 150 125 - 150 6.3 - 7.5  7
2 x 50 125 - 150 250 - 300 12.5 - 15.0  16
1 x 100 125 - 150 125 - 150 12.5 - 15.0  14
2 x 100 125 - 150 250 - 300 25.0 - 30.0  27
2 x 150 125 - 150 250 - 300 37.5 - 45.0  40
2 x 250 125 - 150 250 - 300 62.5 - 75.0  60
*Based on performance specifications provided by the manufacturer. Output may vary depending on sample quality, cluster density and other experimental factors.
Summary of the table's contents

Illumina MiSeq Standard (MiSeq v2/v3 chemistry, 1 lane per flowcell)
Read length [bases]Sequenced fragments per lane* [millions]Reads per lane* [millions]Output per lane* [giga bases]Approx. runtime [hours]
1 x 50 12 - 15 12 - 15  0.6 - 0.8  4
2 x 75 22 - 25 44 - 50  3.3 - 3.8  21
2 x 150 12 - 15 24 - 30 3.6 - 4.5  24
2 x 250 12 - 15 24 - 30 6.0 - 7.5  39
2 x 300 22 - 25 44 - 50 13.2 - 15.0  56
*Based on performance specifications provided by the manufacturer. Output may vary depending on sample quality, cluster density and other experimental factors.
Summary of the table's contents

Illumina MiSeq Micro (MiSeq v2 chemistry, 1 lane per flowcell)
Read length [bases]Sequenced fragments per lane* [millions]Reads per lane* [millions]Output per lane* [giga bases]Approx. runtime [hours]
 2 x 150  3 - 4  6 - 8  0.9 - 1.2  24
*Based on performance specifications provided by the manufacturer. Output may vary depending on sample quality, cluster density and other experimental factors.
Summary of the table's contents

Illumina MiSeq Nano (MiSeq v2 chemistry, 1 lane per flowcell)
Read length [bases]Sequenced fragments per lane* [millions]Reads per lane* [millions]Output per lane* [giga bases]Approx. runtime [hours]
 2 x 150  0.8 - 1  1.6 - 2 0.2 - 0.3  24
 2 x 250  0.8 - 1  1.6 - 2 0.2 - 0.3   39
*Based on performance specifications provided by the manufacturer. Output may vary depending on sample quality, cluster density and other experimental factors.
Summary of the table's contents

Internal users can find information regarding costs for these services on Pricing (behind login).

Data analysis

We maintain high-performance computing workflows for the analysis of large-scale sequencing data sets obtained from a wide range of next-generation sequencing applications. These currently include variant detection from targeted and whole-genome sequencing, expression quantification, de novo assembly of pathogen genomes, protein-DNA interaction detection, methylation profiling and metagenomic profiling.

We have dedicated access to computer nodes, secure and backed-up storage at the Imperial High-Performance Computing Service and the Imperial Data Centre. In order to facilitate the interpretation, visualisation and mining of genomic data, we provide access to a local mirror of the UCSC genome browser and have a licence for the Human Gene Mutation Database Professional. We also assist with the submission of sequencing and variant data to the relevant archives for publication.

For pricing information, please contact us for a quotation.