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lecture_notes:04-05-2010 [2010/04/05 22:29] hyjkim |
lecture_notes:04-05-2010 [2010/04/07 18:22] galt |
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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 | ||
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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===== |