Banana Slug Genomics

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====== 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 =====
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~~REFNOTES cite~~
Banana Slug Genomics

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