lecture_notes:04-05-2010
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lecture_notes:04-05-2010 [2010/04/07 18:22] galt |
lecture_notes:04-05-2010 [2010/04/16 00:46] 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]] | ||
| - | [[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]] | + | 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. | ||
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| + | 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: 2010/04/16 01:16 by karplus
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