The Illumina GA II Sequencing System

Werner Van Belle¹^* - werner@yellowcouch.org, werner.van.belle@gmail.com

1- Deep Sequencing Unit Department of Biosystems Science and Engineering ETH Zurich; Mattenstrasse 24, Building 1058, Basel; Switzerland

Abstract : In this talk I present the Illumina software pipeline 1.0. This pipeline analyzes output from the GA2 sequencing by synthesis analysis system and produces 4 major outputs: intensity files, sequences, alignments and various error reports. Next to the overall pipeline layout I present a number of usage scenarios and document how they are realized within the pipeline.

Keywords: deep sequencing illumina software engineering
Reference: Werner Van Belle; The Illumina GA II Sequencing System; Presented at Department of Computer Science; ETH Zurich; Zurich; Switzerland; October 2008

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