User Tools

Site Tools


archive:review_articles

Differences

This shows you the differences between two versions of the page.

Link to this comparison view

Next revision
Previous revision
archive:review_articles [2010/04/07 15:45]
galt created
archive:review_articles [2015/07/27 22:59] (current)
ceisenhart ↷ Page moved from review_articles to archive:review_articles
Line 1: Line 1:
-=== Assemblers ​Review Articles ====+====== Review Articles ​======
  
 +===== (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.
 +
 +
 +  * ** 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.1270680308.txt.gz · Last modified: 2010/04/07 15:45 by galt