DNA Pipelines Operations

DNA Pipelines Operations

The Wellcome Sanger Institute's technological platforms underpin our ability to carry out biomedical research on a large scale, allowing researchers to answer questions that can be intractable in other institutions.

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Here we outline the operation of these platforms and discuss how researchers can access our technologies.

The Wellcome Sanger Institute was founded to exploit DNA sequence in order to understand biology and disease.

That imperative remains as strong today as the Institute capitalises on leading-edge technologies to answer questions that were unanswerable only a few years ago. We have always used and will continue to use the most appropriate technology to provide the data that solve important questions in biomedicine.

The Institute has one of the largest DNA sequencing facilities in the world. Our nextgeneration sequencing capacity is currently at XX Illumina HiSeqs (comprising 10 HiSeq 2500 V4 and XX HiSeq2000 V3) , 10 HiSeq X machines (‘X Ten’), 5 Illumina MiSeqs, one PacBio RSII and one PacBio Sequel machine. For large-scale genotyping, there are 5 Illumina iScan machines and three Agena mass spectrometers. The DNA Pipelines are further supported by an automated sample management lab. The facility is capable of producing more than 1700 terabases (1700 x 1012 bp) of DNA sequence per year.

DNA Pipelines provides genome analysis services for the Institute’s Faculty. The Pipelines process DNA, RNA and tissue samples received from internal and external sources to generate sequence, genotype and copy number information. The Operations group oversees the delivery of this high-quality data via a range of technologies and platforms.

DNA Pipelines Operations is split into

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  • Technical Administration
  • Sample Management
  • DNA products
  • RNA products
  • Bespoke products
  • Single Cell Operations
Sample Management

The Sample Management pipeline registers and processes more than 350,000 samples per year. It provides extraction of DNA and RNA from biological materials and delivers automated high-throughput DNA quantification and normalisation. Sample management serves the needs of Faculty members, Celllular Genetics and Phenotyping and the downstream product teams.

Illumina Sequencing

The Illumina Sequencing platform uses Illumina Miseqs, HiSeqs, HiSeqX's and HiSeq 4000's to generate data through our DNA, RNA and bespoke product teams. The capacity of these machines allows the teams to combine multiple sample libraries into a single lane, routinely generating more than 1Tb per run.

Typically, our Libraries now meet a 99.8 per cent pass rate and a reduction in sequencing lane failure rates to less than 5 per cent.


The PacBio next-generation platform supports research projects that require longer read lengths, such as bacterial and parasite de-novo sequencing and viral sequencing.


The Genotyping Pipelines use the Illumina and Agena platforms, which includes five high-resolution Illumina bead chip scanners (iScans) and three Agena mass spectrometers. In all, the Institute has the capacity for 110,000 genome-wide scans and 500,000 Agena low plex types per year. A large part of the Pipelines’ work has focused on collaborative projects, including WTCCC3, which is a consortium study funded by the Wellcome Trust.

Optical Mapping

The Optical Mapping platform provides services using the BioNano Irys system.