Banana Slug Genomics

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

>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, and roughly 35-100 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.
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//Text from a draft of Jenny Draper's Doctoral Thesis.  **Please change.**//  --- //[[learithe@soe.ucsc.edu|Jenny Draper]] 2010/03/30 17:14//

Banana Slug Genomics

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