genepool

Next Generation Sequencing and Bioinformatics
at the University of Edinburgh


Our delivery goals: high quality data and best-practice analyses

The GenePool is a research facility. We perform genomic sequencing and analysis in collaboration with academic users. We aim to deliver high quality data and analyses to our collaborators. We measure the quality of what we deliver by user satisfaction, and thus aim to meet or exceed user requirements.

 

Illumina GAIIx and HiSeq 2000: data volumes
On the GAIIx platform, we currently aim to generate at least 20 million single-end reads (40 million paired-end reads) per lane (there are seven available lanes in a flow cell). A GAIIx flow cell lane can deliver up to 30 million reads, but this is sometimes at the cost of overall quality. On the HiSeq 2000 system, we aim to generate at least 45 million single-end reads (90 million paired-end reads) per lane using the v2 sequencing chemistry, and at least 150 million single-end reads (300 million paired-end reads) per lane using the v3 reagents. We will sometimes seed lanes at lower densities for titration and other operational reasons, but will deliver at least the number of reads or coverage specified in our quote. Please note that we cannot guarantee yield for samples delivered to us as fragment libraries ready for sequencing, although we will always endeavour to generate the best data possible.


Roche 454 Titanium: data volumes
A run on the Titanium version of the instrument and reagents delivers up to 800,000 reads of average length 350-450 bases from genomic libraries (other types of sample, e.g. cDNA samples, may generate shorter reads). We offer part-run volumes to users, but these are at the price of fewer reads overall (e.g. an eighth of a run generates ~80,000 reads). Please note that we cannot guarantee yield for samples delivered to us as custom cDNA libraries or fragment/amplicon libraries ready for sequencing, although we will always endeavour to generate the best data possible.


Sequencing project timing
The GenePool delivers sequencing to hundreds of users across the UK and we are very busy. We make strategic investments in staff and instruments to ensure that our sequencers are running as fast as we can make them. Our Technologists will be able to advise you on the length of time the current queue represents. Samples are regarded as being in the queue when they are delivered and we have confirmed that they are suitable for sequencing after quality control. Please note that we do not book space for samples in advance.


The preparation, sequencing and bioinformatics processing of samples take time. The workflow of the process has also to be scheduled with respect to instrument capacity, staff availability and the queue of user samples. On receipt of your samples with a valid samples submission form, we will email the designated contact person to acknowledge receipt and to give a first estimate of when the samples are expected to be processed (i.e. their place in the queue).


The Illumina workflow: Library preparation for the Illumina GAIIx and HiSeq 2000 platforms takes from 1 to 7 working days. Multiple samples can be prepared at one time, but large sample sets may take several weeks to process. The run time on the sequencers is up to 7 working days for a single-end run, and up to 10 working days for a paired-end run. Basic bioinformatics processing takes up to 5 working days depending on sample type. Taking into account QC steps and other operational constraints, it will be at least 6 weeks from initiating the processing of a single sample before preliminary results are available. We will email the designated contact person when the samples are loaded onto the sequencing instrument to keep you informed of progress. If the run or the sample has performed below our stringent quality criteria, we will inform the designated contact person, and usually re-sequence the sample (at no extra cost to you) on the next available sequencing run.


The Roche 454 Titanium workflow: Preparation of sequencing libraries for the Roche 454 platform can take from one working day (genomic DNA samples) to six weeks (RNA samples for generation of normalised cDNA). The clonal amplification and sequencing process takes at least a week, including titration and QC steps. Please allow a minimum of 4 weeks from receipt of the sample before we deliver the data to you.


Bioinformatics workflow: Once high quality data are generated, we will perform the basic bioinformatics analyses required. If you have requested additional bioinformatics analyses, we will provide you with an estimate of the timeframe for completion of these tasks.

 

 

 



The GenePool has core support from: GenePool admin site
edinburgh
The University of Edinburgh
School of Biological Sciences
The Darwin Trust
of Edinburgh
darwin
mrc
nerc
bbsrc
sulsa

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This is version 2.2 of the GenePool website (July 2009).