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(Next-Gen) Sequencing review articles
Assembler review articles
Assembly algorithms for next-generation sequencing data
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.
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.
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.