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====== Brief overview of goals and data input characteristics ====== Kevin laid out some of the logistics of the class. A broad goal: For each chromosome in the slug, we want the full sequence in DNA bases. Since it is unlikely to be completed in the timeframe of one quarter, some smaller goals: build contigs and have an idea of the scaffold to arrange the contigs in. Inputs: Sequencing data from various machines. Some of the characteristics of these machines/techniques: ==== Sanger capillary ==== * ~800bp reads[(cite:wikisanger>http://en.wikipedia.org/wiki/Microfluidic_Sanger_sequencing)]. * Q (quality value) ~30 * ~$1/read, expensive because primers must be attached to each read. ==== 454 ==== * ~400bp reads[(cite:wiki454>http://en.wikipedia.org/wiki/454_Life_Sciences)]. * Pyrosequencing * Q ~20 * $5000/run/~1m reads, no downscaling (numbers approximate). ==== SoLiD ==== * 2x25bp or 1x50bp reads * Paired end reads: ligation with adapter, cleaves 25bp from adapter using restriction enzyme. * Potential for double ligation: two unrelated sequences ligating. * $2000/run/100m reads (numbers approximate). ==== Illumina ==== ==== Ion Torrent ==== ==== Pac Bio ==== ===== References ===== <refnotes>notes-separator: none</refnotes> ~~REFNOTES cite~~
