lecture_notes:03-30-2011
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lecture_notes:03-30-2011 [2011/03/30 23:05] eyliaw |
lecture_notes:03-30-2011 [2011/04/01 03:56] svohr [Ion Torrent] |
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| Inputs: Sequencing data from various machines. Some of the characteristics of these machines/techniques: | Inputs: Sequencing data from various machines. Some of the characteristics of these machines/techniques: | ||
| - | ===== Sanger capillary ===== | + | ==== Sanger capillary ==== |
| - | + | * ~800bp reads[(cite:wikisanger>http://en.wikipedia.org/wiki/Microfluidic_Sanger_sequencing)]. | |
| - | 454 | + | * Q (quality value) ~30 |
| - | SoLiD | + | * ~$1/read, expensive because primers must be attached to each read. |
| - | Illumina | + | ==== 454 ==== |
| - | Ion Torrent | + | * ~400bp reads[(cite:wiki454>http://en.wikipedia.org/wiki/454_Life_Sciences)]. |
| - | Pac Bio | + | * 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 ==== | ||
| + | * 2x50, 2x100bps ? | ||
| + | * Paired end reads | ||
| + | * Potential errors: innies (ligated region not between sequenced regions) or chimeric (sequence passes ligated region) | ||
| + | * Cheaper than SoLiD, 10K Genomes project uses it. | ||
| + | ==== Ion Torrent ==== | ||
| + | * 2x100 base pairs | ||
| + | * ~50,000 to 5,000,000 reads depending on Sequencing Chip [(cite:ionTorrent>http://www.iontorrent.com/technology-how-does-it-perform/)]. | ||
| + | * Ion semiconductor sequencing. No optics or modified bases are required. | ||
| + | ==== Pac Bio ==== | ||
| + | * Very long, single molecule reads (~10K) | ||
| + | * High error rates (~5%) | ||
| + | * Useful when mapping to a reference. | ||
| + | ===== References ===== | ||
| + | <refnotes>notes-separator: none</refnotes> | ||
| + | ~~REFNOTES cite~~ | ||
lecture_notes/03-30-2011.txt · Last modified: 2011/04/01 19:20 by svohr
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