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lecture_notes:04-05-2010 [2010/04/07 18:45] 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 | ||
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* [[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]] | * [[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 | + | Jason R. Miller, Sergey Koren and Granger Suttona |
- | + | ||
- | Covers these assemblers: SSAKE, SHARCGS, VCAKE, Newbler, Celera Assembler, Euler, Velvet, ABySS, AllPaths, and SOAPdenovo. | + | Covers these assemblers: SSAKE, SHARCGS, VCAKE, Newbler, Celera, Euler, Velvet, ABySS, AllPaths, and SOAPdenovo. |
- | + | ||
- | Compares de Bruijn graph to overlap/layout/consensus. | + | 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. | + | Jason R. Miller, Sergey Koren, Granger Sutton, Assembly algorithms for next-generation sequencing data, Genomics, |
- | (http://www.sciencedirect.com/science/article/B6WG1-4YJ6GD8-1/2/ae6c957910e4ea658cdebff4a0ce9793) | + | In Press, Corrected Proof, Available online 6 March 2010, ISSN 0888-7543, DOI: 10.1016/j.ygeno.2010.03.001. |
- | Keywords: Genome assembly algorithms; Next-generation sequencing | + | (http://www.sciencedirect.com/science/article/B6WG1-4YJ6GD8-1/2/ae6c957910e4ea658cdebff4a0ce9793) |
+ | Keywords: Genome assembly algorithms; Next-generation sequencing | ||
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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? |