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Review Articles

(Next-Gen) Sequencing review articles

  • Sequencing technologies — the next generation [1]
    Comparison of technologies and some applications.
  • Uncovering the roles of rare variants in common disease through whole-genome sequencing [2]
    Using next generation sequencing to diagnosis/understand human diseases.

Assembler review articles

  • Assembly algorithms for next-generation sequencing data [3]
    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. [4]
    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

1. a 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
2. a 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
3. a 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.
4. a 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

Discussion

, 2010/04/11 15:46

References should use the refnotes plugin (see the style page)

, 2010/04/12 17:40

The formatting has been fixed; everyone please follow the new format. Use the level 2 header ( ====== ) for the categorization of review articles (e.g. Assembler review articles) and use bold for paper titles followed by a RefNotes citation for that paper (the paper titles use bold since the heading syntax does not work when followed by a RefNotes citation). When adding new review articles, please place them in alphabetical order. Any notes or information about the review article follows the title and reference for the paper.

, 2010/04/08 23:27

The link works for me, but then I created it.

You can also try the link that appears further down in the citation:

http://www.sciencedirect.com/science/article/B6WG1-4YJ6GD8-1/2/ae6c957910e4ea658cdebff4a0ce9793

Of course, if you are off-campus, you will need to use OCA Bookmarkelet from library with your library card, or some other UCSC library mechanism.

, 2010/04/08 16:30

Broken link?

, 2010/04/07 15:50

Actually, if someone knows a better way to format this, please help.

, 2010/04/11 15:31

If we also include a section header, then once we get a lot of articles on this page there will be a table of contents linking to everything.

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archive/review_articles.txt · Last modified: 2015/07/27 22:59 by ceisenhart