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archive:review_articles [2010/04/11 15:30]
jstjohn
archive:review_articles [2015/07/27 22:59] (current)
ceisenhart ↷ Page moved from review_articles to archive:review_articles
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-===== Assemblers ​Review Articles ======+=====Review Articles ======
  
- ===Assembly algorithms for next-generation sequencing data=== +===== (Next-Gen) Sequencing 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]+  * ** 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. 
-  ​ 
-  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.
 +
 +
 +
 +===== 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.
 +
 +
 +
 +
 +===== References =====
 +<​refnotes>​notes-separator:​ none</​refnotes>​
 +~~REFNOTES cite~~
archive/review_articles.1271025009.txt.gz · Last modified: 2010/04/11 15:30 by jstjohn