Banana Slug Genomics

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====== Illumina (formerly Solexa) ======

//Text from a draft of Jenny Draper's Doctoral Thesis.  **Please change.**//  --- //[[learithe@soe.ucsc.edu|Jenny Draper]] 2010/03/30 17:14//
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The [[http://www.illumina.com/|Illumina]] “Genome Analyzer” platform, often referred to as “Solexa” after the company which initially licensed the technology,  utilizes a “bridge PCR” method combined with the “sequencing by synthesis” technique((Shendure, J. & Ji, H. Next-generation DNA sequencing. Nat Biotech 26, 1135-1145 (2008).)). The sample sequences, flanked by ligated adaptors, are hybridized to slide-bound primers at both the 5’ and 3’ ends. Rounds of PCR are initiated, in which the bound sequences are amplified, denatured, and amplified again; in each round one end of the sequence remains tethered to the slide, resulting in clusters of identical sequences similar to the 454 and SOLiD “polony” beads. Sequencing then occurs in a stepwise fashion similar to that of classic Sanger sequencing:  polymerase attaches one of a mixture of 4 dNTPs carrying a reversible chain-terminating fluor; the color incorporated in each spot on the slide is recorded, the fluor is removed, and the cycle continues.  

The latest Illumina platform, the HiSeq 2000, can produce read lengths from 35 to 100bp, producing 26-200 gigabases of data per run, respectively((HiSeq 2000. @ http://www.illumina.com/systems/hiseq_2000.ilmn)). Base-pair substitutions are the most common form of read error with this method. Like SOLiD, it suffers from short read length, making genome assembly based solely on this technology difficult.

Banana Slug Genomics

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