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lecture_notes:04-05-2010 [2010/04/05 15:10]
hyjkim
lecture_notes:04-05-2010 [2010/04/15 17:46]
learithe
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 Please add to or modify this page as you see fit! Please add to or modify this page as you see fit!
 +=====Homework=====
 +Pick two or three assemblers.
 +  * Find out where to get them
 +  * How to install them
 +  * What papers there are about them
 +  * Create the wiki page about them
 +  * And possibly install them
 +
 +Volunteers:
 +  * Phrap: Galt and Shyamini
 +  * Velvet: Hyunsung and Galt 
 +  * ABySS: Galt and Chris
 +  * AMOS: Shyamini and Herbert
 +  * Arachne: John and Michael
 +  * CAP3/PCAT: Michael and Galt
 +  * Celera: Shyamini and Hyunsung
 +  * Euler/​Euler-sr:​ Herbert and John
 +  * MIRA1: Herbert and Michael
 +  * TIGR Assembler: John and Shyamini
 +  * SHARCGS: Michael and Chris
 +  * SSAKE: Herbert and Hyunsung
 +  * Staden gap4 package: Michael and Hyunsung
 +  * VCAKE: Chris and John
 +  * Phusion: Shyamini and Michael
 +  * QSRA: Herbert and Chris
 +  * SOLiD System Tools (Corona_lite,​ etc): Hyunsung and Chris
 +  * 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]]
 +
 +  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 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 ยท Last modified: 2010/04/15 18:16 by karplus