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lecture_notes:03-30-2011 [2011/03/30 23:16] 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:sangerwiki>http://en.wikipedia.org/wiki/Microfluidic_Sanger_sequencing)]. | + | * ~800bp reads[(cite:wikisanger>http://en.wikipedia.org/wiki/Microfluidic_Sanger_sequencing)]. |
- | Q (quality value) ~30 | + | * Q (quality value) ~30 |
- | Expensive (~$1/read) because primers must be attached to each read. | + | * ~$1/read, expensive because primers must be attached to each read. |
==== 454 ==== | ==== 454 ==== | ||
- | ~500bp reads[(cite:454wiki>http://en.wikipedia.org/wiki/454_Life_Sciences)]. | + | * ~400bp reads[(cite:wiki454>http://en.wikipedia.org/wiki/454_Life_Sciences)]. |
- | Pyrosequencing | + | * Pyrosequencing |
- | $5000/run/~1m reads | + | * Q ~20 |
+ | * $5000/run/1M reads, no downscaling (numbers approximate). | ||
==== SoLiD ==== | ==== 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 ==== | ==== 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 ==== | ==== 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 ==== | ==== Pac Bio ==== | ||
+ | * Very long, single molecule reads (~10K) | ||
+ | * High error rates (~5%) | ||
+ | * Useful when mapping to a reference. | ||
===== References ===== | ===== References ===== | ||
<refnotes>notes-separator: none</refnotes> | <refnotes>notes-separator: none</refnotes> | ||
~~REFNOTES cite~~ | ~~REFNOTES cite~~ |