If you are based in WHG, in four easy steps you can gain access to a desktop next generation sequencing platform that supports a variety of applications offering simple, rapid, and affordable generation of sequence data for a wide variety of project types.
All users will require basic training before they may run either the MiSeq or the NextSeq 500 unaided. Training will entail an overview of the system requirements, the provision of relevant user guides, and that the user’s first run will be performed with a member of OGC. You can request training or information by contacting firstname.lastname@example.org. Please note, due to specific considerations, it is advisable to contact OGC before preparing Illumina libraries for either platform (e.g. please see the Index Adaptors Pooling Guide and the support Bulletin-Library pooling guidelines for the NextSeq and MiniSeq systems, which can be downloaded from the Illumina website).
You will also need an Illumina BaseSpace account as data will be sent directly to BaseSpace. No external drives will be connected to either system.
Setup a BaseSpace account.
In addition, you will need to download the Illumina Experiment Manager (IEM) from the Illumina website. This program is used to generate the sample sheet for the run.
We use ARIA, developed by the Division of Structural Biology at Oxford University (STRUBI) as the booking platform for this service.
|150PE or less||250PE||300PE||All mid or 75PE high output||150PE high ouput|
|MiSeq||£100, 1 slot||£200, 2 slots||£300, 3 slots||N/A||N/A|
|NextSeq||N/A||N/A||N/A||£200, 1 run slot||£400, 2 slots|
Logon to ARIA, view the calendar for availability, and request a run slot. Provide a PO number for payment and submit. You will be notified within 1 working day that your run slot is approved or if there is a problem. If you need to book a run less than 1 day in advance, please e-mail email@example.com to notify us of the booking.
At the end of each month, usage will be recharged to the appropriate PO number. In the first instance, no formal restriction will be placed on the number of run slots that can be booked and it is hope that internal users will work together to ensure fair and optimal usage.
To run the machine, you will need to arrive with the following:
N.B. It is essential that your start runs at a time that fits within your booked slot. Currently, runs are expected to be on the machine and started by 12:00pm of the first day of the run slot(s) booked. This is to ensure that all runs are finished before the next slot opens, and to allow time in between runs for routine maintenance on the machine.
Should the either system fail, all bookings will be adjusted in line with the number of days the platform is not operational.
|NextSeq 500 System Performance Parameters|
|Flow Cell Configuration||Read Length (bp)||Output (Gb)||Run Time (Hours)||Data Quality||Kit Catalogue #|
|High-Output Flow Cell
Up to 400 M paired-end reads*
|2 x 150||100-120||29||> 75% > Q30||FC-404-2004|
|2 x 75||50-60||18||> 80% > Q30||FC-404-2002|
|1 x 75||25-30||11||> 80% > Q30||FC-404-2005|
|Mid-Output Flow Cell
Up to 130 M paired-end reads*
|2 x 150||32-39||26||> 75% > Q30||FC-404-2003|
|2 x 75||16-19||15||> 80% > Q30||FC-404-2001|
|* Yields are for optimised PhiX runs and therefore represent a maximum possible yield on this platform.|
|MiSeq System Performance parameters|
|Flow Cell Configuration||Reda Length (bp)||Output (Gb)*||Run Time (Hrs)||Data Quality||Kit Catalogue No.|
|Standard MiSeq v2||1 x 36||0.54-0.61||4||>90% bases higher than Q30||MS-102-2001|
|2 x 25||0.75-0.85||5.5||>90% bases higher than Q30||MS-102-2001|
|2 x 150||4.5-5.1||24||>80% bases higher than Q30||MS-102-2002|
|2 x 250||7.5-8.5||39||>75% bases higher than Q30||MS-102-2003|
|Standard MiSeq v3||2 x 75||3.3-3.8||21||>85% bases higher than Q30||MS-102-3001|
|2 x 300||13.2-15||56||>70% bases higher than Q30||MS-102-3003|
|Micro v2||2 x 150||1.2||19||>80% bases higher than Q30||MS-103-1002|
|Nano v2||2 x 150||0.3||17||>80% bases higher than Q30||MS-103-1001|
|2 x 250||0.5||28||>75% bases higher than Q30||MS-103-1003|
* Yields are optimised PhiX runs.
A bcl –> fastq conversion of data can be carried out in BaseSpace, prior to download of data to your own file storage system. Please note you will have to make your own arrangements for data storage and downstream processing. Read more about our in-house data processing.
If you do not want to make your own libraries OGC can help. OGC-prepared libraries will be QC-ed and provided at 10nM concentration where possible. Please contact OGC for a quotation.
If you are happy to wait a little longer OGC also offers a full-service option using these platforms. The advantages to you of this full-service option are decades of combined experience in next-generation sequencing that maximises output and data quality from Illumina technology, access to the full OGC data QC and project-specific analytical pipelines, and access to a group of dedicated project managers to help plan your project – taking the stress out of generating data.
All relevant Illumina documentation can be downloaded from the following website: