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lecture_notes:04-05-2010 [2010/04/07 11:27]
galt
lecture_notes:04-05-2010 [2010/04/15 17:46]
learithe
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   * SOLiD System Tools (Corona_lite,​ etc): Hyunsung and Chris   * SOLiD System Tools (Corona_lite,​ etc): Hyunsung and Chris
   * Newbler documentation:​ Galt and Herbert   * Newbler documentation:​ Galt and Herbert
 +  * SOAPdenovo: Galt and Jenny
  
  
 +Assembly Review Articles:
 +  * [[http://​www.sciencedirect.com/​science?​_ob=ArticleURL&​_udi=B6WG1-4YJ6GD8-1&​_user=10&​_coverDate=03%2F06%2F2010&​_rdoc=1&​_fmt=high&​_orig=search&​_sort=d&​_docanchor=&​view=c&​_searchStrId=1282691739&​_rerunOrigin=google&​_acct=C000050221&​_version=1&​_urlVersion=0&​_userid=10&​md5=32c08d11cc10fd1eefca0f8a8def738b|Assembly algorithms for next-generation sequencing data]]
  
-[[http://​www.sciencedirect.com/​science?​_ob=ArticleURL&​_udi=B6WG1-4YJ6GD8-1&​_user=10&​_coverDate=03%2F06%2F2010&​_rdoc=1&​_fmt=high&​_orig=search&​_sort=d&​_docanchor=&​view=c&​_searchStrId=1282691739&​_rerunOrigin=google&​_acct=C000050221&​_version=1&​_urlVersion=0&​_userid=10&​md5=32c08d11cc10fd1eefca0f8a8def738b|Review Article]]+  Jason R. Miller, Sergey Koren and Granger Suttona 
 +   
 +  Covers these assemblers: SSAKE, SHARCGS, VCAKE, Newbler, Celera, Euler, Velvet, ABySS, AllPaths, and SOAPdenovo. 
 +   
 +  Compares de Bruijn graph to overlap/​layout/​consensus. 
 +   
 +  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) 
 +  Keywords: Genome assembly algorithms; Next-generation sequencing
  
- ​Assembly algorithms for next-generation sequencing data 
  
- Jason R. Miller, Sergey Korena and Granger Suttona 
- 
- ​SSAKE,​ SHARCGS, VCAKE, Newbler, Celera Assembler, Euler, Velvet, ABySS, AllPaths, and SOAPdenovo. 
- 
- More generally, it compares the two standard methods known as the de Bruijn graph approach and the overlap/​layout/​consensus approach to assembly. 
  
 =====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. ​(see comment below)
     * 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?
lecture_notes/04-05-2010.txt · Last modified: 2010/04/15 18:16 by karplus