Illumina/Solexa Genome Analyzer (GA) can generate about 75 bp
DNA sequencing read length and more than 300 million reads per flow cell. It enables a broad range of high-throughput sequencing applications for genomic discovery and validation. These include DNA sequencing, gene regulation, sequencing-based transcriptome analysis, SNP discovery and structural variation analysis, Chip-Seq, etc. This tutorial will briefly introduce GA technology and potential applications, then will focus on data process and data analysis. We will also cover sequence assembly with Velvet, sequence mapping with Bowtie, and transcriptome analysis with GenomeStudio RNA sequencing module, etc.