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archive:review_articles [2010/04/07 22:47] galt |
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- | === Assemblers Review Articles ==== | + | ====== 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]] | + | ===== (Next-Gen) Sequencing review articles ====== |
+ | * ** Sequencing technologies — the next generation **[(cite:metzker>Michael L. Metzker. Sequencing technologies — the next generation. //Nature Reviews Genetics// **11**, 31-46 (January 2010) | doi:10.1038/nrg2626. http://www.nature.com/nrg/journal/v11/n1/full/nrg2626.html)] \\ Comparison of technologies and some applications. | ||
- | 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 | ||
+ | * ** Uncovering the roles of rare variants in common disease through whole-genome sequencing **[(cite:cirulli>Elizabeth T. Cirulli and David B. Goldstein. Uncovering the roles of rare variants in common disease through whole-genome sequencing. //Nature Reviews Genetics// **11**, 415-425 (June 2010) | doi:10.1038/nrg2779. http://www.nature.com/nrg/journal/v11/n6/full/nrg2779.html)] \\ Using next generation sequencing to diagnosis/understand human diseases. | ||
+ | ===== Assembler review articles ====== | ||
+ | |||
+ | * ** Assembly algorithms for next-generation sequencing data **[(cite:assem_alg>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:[[http://dx.doi.org/10.1016/j.ygeno.2010.03.001|10.1016/j.ygeno.2010.03.001]].)] \\ 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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+ | ===== Technology review articles ====== | ||
+ | * ** Computational methods for discovering structural variation with next-generation sequencing. **[(cite:tech>Medvedev P, Stanciu M, Brudno M. Computational methods for discovering structural variation with next-generation sequencing. //Nat Methods//,2009 Nov 6 (11 Suppl):S13-20.http://www.nature.com/nmeth/journal/v6/n11s/abs/nmeth.1374.html)] \\ A good 2009 review article **on the state of paired-end sequencing**. Includes some discussion of the difference between mate-pair and paired-end reads, the many types of of contig linkages they can produce, as well as discussion about data prossessing and available tools. | ||
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+ | ===== References ===== | ||
+ | <refnotes>notes-separator: none</refnotes> | ||
+ | ~~REFNOTES cite~~ |