title: Genome-guided transcriptome assembly in the age of next-generation sequencing.
abstract: 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.
authors: Liliana D
authors: LD
authors: Florea
authors: Steven L
authors: SL
authors: Salzberg
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D002874:Chromosome Mapping / Q000379:methods*; D003198:Computer Simulation; D016678:Genome / Q000235:genetics*; D008957:Models, Genetic; D008969:Molecular Sequence Data; D017423:Sequence Analysis, RNA / Q000379:methods*; D059467:Transcriptome / Q000235:genetics*