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Issue No.05 - Sept.-Oct. (2013 vol.10)
pp: 1234-1240
Published by the IEEE Computer Society
Liliana D. Florea , Johns Hopkins University School of Medicine, Baltimore
Steven L. Salzberg , Johns Hopkins School of Medicine and Bloomberg School of Public Health, Baltimore
Next generation sequencing technologies provide unprecedented power to explore the repertoire of genes and their alternative splice variants, collectively defining the transcriptome of a species in great detail. However, assembling the short reads into full-length gene and transcript models presents significant computational challenges. We review current algorithms for assembling transcripts and genes from next generation sequencing reads aligned to a reference genome, and lay out areas for future improvements.

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