lecture_notes:04-05-2010
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lecture_notes:04-05-2010 [2010/04/05 22:10] hyjkim |
lecture_notes:04-05-2010 [2010/04/07 18:22] galt |
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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 | ||
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| + | [[Review Article | 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 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===== | ||
lecture_notes/04-05-2010.txt ยท Last modified: 2010/04/16 01:16 by karplus
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