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lecture_notes:04-05-2010 [2010/04/05 15:29]
hyjkim
lecture_notes:04-05-2010 [2010/04/15 18:16] (current)
karplus fixed citations to use Refnotes syntax
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 Volunteers: Volunteers:
-Phrap: Galt and Shyamini +  * Phrap: Galt and Shyamini 
-Velvet: Hyunsung and Galt  +  ​* ​Velvet: Hyunsung and Galt  
-ABySS: Galt and Chris +  ​* ​ABySS: Galt and Chris 
-AMOS: Shyamini and Herbert +  ​* ​AMOS: Shyamini and Herbert 
-Arachne: John and Michael +  ​* ​Arachne: John and Michael 
-CAP3/PCAT: Michael and Galt +  ​* ​CAP3/PCAT: Michael and Galt 
-Celera: Shyamini and Hyunsung +  ​* ​Celera: Shyamini and Hyunsung 
-Euler/​Euler-sr:​ Herbert and John +  ​* ​Euler/​Euler-sr:​ Herbert and John 
-MIRA1: Herbert and Michael +  ​* ​MIRA1: Herbert and Michael 
-TIGR Assembler: John and Shyamini +  ​* ​TIGR Assembler: John and Shyamini 
-SHARCGS: Michael and Chris +  ​* ​SHARCGS: Michael and Chris 
-SSAKE: Herbert and Hyunsung +  ​* ​SSAKE: Herbert and Hyunsung 
-Staden gap4 package: Michael and Hyunsung +  ​* ​Staden gap4 package: Michael and Hyunsung 
-VCAKE: Chris and John +  ​* ​VCAKE: Chris and John 
-Phusion: Shyamini and Michael +  ​* ​Phusion: Shyamini and Michael 
-QSRA: Herbert and Chris +  ​* ​QSRA: Herbert and Chris 
-SOLiD System Tools (Corona_lite,​ etc): Hyunsung and Chris+  ​* ​SOLiD System Tools (Corona_lite,​ etc): Hyunsung and Chris 
 +  * Newbler documentation:​ Galt and Herbert 
 +  * SOAPdenovo: Galt and Jenny
  
 +
 +Assembly Review Articles:
 +  * Jason R. Miller, Sergey Koren and Granger Suttona [(cite:​Miller2010>​Jason R. Miller, Sergey Koren, Granger Sutton, Assembly algorithms for next-generation sequencing data, Genomics, In Press, Corrected Proof, Available online 6 March 2010, ISSN 0888-7543, DOI: 10.1016/​j.ygeno.2010.03.001 http://​www.sciencedirect.com/​science/​article/​B6WG1-4YJ6GD8-1/​2/​ae6c957910e4ea658cdebff4a0ce9793)] \\ Covers these assemblers: SSAKE, SHARCGS, VCAKE, Newbler, Celera, Euler, Velvet, ABySS, AllPaths, and SOAPdenovo.Compares de Bruijn graph to overlap/​layout/​consensus.
 +  ​
 + 
 =====Assembly Overview===== =====Assembly Overview=====
  
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       * Expect half your reads to have an error in them.       * Expect half your reads to have an error in them.
   * Contiguous chromosomes with a low error rate ( output from assemblers).   * Contiguous chromosomes with a low error rate ( output from assemblers).
-    * Miami standard for a finished genome should have an error rate of 1 x 10^-5 bases.+    * Bermuda ​standard for a finished genome should have an error rate of 1 x 10^-5 bases.1) [(cite:​Bermuda1>​[[http://​www.genome.gov/​page.cfm?​pageID=10506376]])] [(cite:​Bermuda2>​[[http://​www.ornl.gov/​sci/​techresources/​Human_Genome/​research/​bermuda.shtml]])]
     * To reduce error rate in short reads, stack up many reads and take the most common base at each position.     * To reduce error rate in short reads, stack up many reads and take the most common base at each position.
   * How much data do we have?   * How much data do we have?
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     - Can find repeat regions using paired-end data.     - Can find repeat regions using paired-end data.
   * Most resquencing projects map reads to scaffolds and create contigs based upon mapping. Sections with missing read data can be assumed to be a deleting or an alteration to the existing scaffold.   * Most resquencing projects map reads to scaffolds and create contigs based upon mapping. Sections with missing read data can be assumed to be a deleting or an alteration to the existing scaffold.
 +
 +
 +===== References =====
 +<​refnotes>​notes-separator:​ none</​refnotes>​
 +~~REFNOTES cite~~
 +
 +
lecture_notes/04-05-2010.1270506546.txt.gz · Last modified: 2010/04/05 15:29 by hyjkim