lecture_notes:04-05-2010
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lecture_notes:04-05-2010 [2010/04/05 22:17] hyjkim |
lecture_notes:04-05-2010 [2010/04/13 14:27] learithe |
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| * Create the wiki page about them | * Create the wiki page about them | ||
| * And possibly install 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===== | ||
| Line 32: | Line 70: | ||
| * 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. | + | * Miami standard for a finished genome should have an error rate of 1 x 10^-5 bases. FIXME |
| * 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: 2010/04/16 01:16 by karplus
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