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lecture_notes:03-30-2011 [2011/03/30 23:19] eyliaw |
lecture_notes:03-30-2011 [2011/03/30 23:32] eyliaw [SoLiD] |
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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 | ||
* ~$1/read, expensive because primers must be attached to each read. | * ~$1/read, expensive because primers must be attached to each read. | ||
==== 454 ==== | ==== 454 ==== | ||
- | * ~400bp reads[(cite:454wiki>http://en.wikipedia.org/wiki/454_Life_Sciences)]. | + | * ~400bp reads[(cite:wiki454>http://en.wikipedia.org/wiki/454_Life_Sciences)]. |
- | * Q ~20 | + | |
* Pyrosequencing | * Pyrosequencing | ||
- | * $5000/run/~1m reads, no downscaling. | + | * 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 ==== | ||