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Here's a paper from the Sanger, talking about their experiences and process improvements with the genome analysers:
A large genome center's improvements to the Illumina sequencing system.
Quail ME, Kozarewa I, Smith F, Scally A, Stephens PJ, Durbin R, Swerdlow H, Turner DJ
Nature Methods 2008; 5(12): 1005-10
The Wellcome Trust Sanger Institute is one of the world's largest genome centers, and a substantial amount of our sequencing is performed with 'next-generation' massively parallel sequencing technologies: in June 2008 the quantity of purity-filtered sequence data generated by our Genome Analyzer (Illumina) platforms reached 1 terabase, and our average weekly Illumina production output is currently 64 gigabases. Here we describe a set of improvements we have made to the standard Illumina protocols to make the library preparation more reliable in a high-throughput environment, to reduce bias, tighten insert size distribution and reliably obtain high yields of data.
http://www.nature.com/nmeth/journal/v5/n12/abs/nmeth.1270.html
I think I'll incorporate a few of those things into my next run. Some of them are very simple... for example, avoiding the 50 degrees C melting step during the gel purification. They suggest that it denatures AT rich regions and prevents them from being collected by the subsequent column purification, adding to the bias that is now (I think) well known with the platform. They simply melt their gel at room temperature.
A large genome center's improvements to the Illumina sequencing system.
Quail ME, Kozarewa I, Smith F, Scally A, Stephens PJ, Durbin R, Swerdlow H, Turner DJ
Nature Methods 2008; 5(12): 1005-10
The Wellcome Trust Sanger Institute is one of the world's largest genome centers, and a substantial amount of our sequencing is performed with 'next-generation' massively parallel sequencing technologies: in June 2008 the quantity of purity-filtered sequence data generated by our Genome Analyzer (Illumina) platforms reached 1 terabase, and our average weekly Illumina production output is currently 64 gigabases. Here we describe a set of improvements we have made to the standard Illumina protocols to make the library preparation more reliable in a high-throughput environment, to reduce bias, tighten insert size distribution and reliably obtain high yields of data.
http://www.nature.com/nmeth/journal/v5/n12/abs/nmeth.1270.html
I think I'll incorporate a few of those things into my next run. Some of them are very simple... for example, avoiding the 50 degrees C melting step during the gel purification. They suggest that it denatures AT rich regions and prevents them from being collected by the subsequent column purification, adding to the bias that is now (I think) well known with the platform. They simply melt their gel at room temperature.