from Nature Biotechnology
Two methods for de novo transcriptome assembly of short reads were published this year from Lior Pachter and colleagues1 and from Aviv Regev and colleagues2. The transcriptome can be analyzed by sequencing cDNA reverse transcribed from RNA (RNA-Seq), but mapping and assembling the resulting reads are challenging owing to the complexities introduced by RNA splicing. The two methods are the first that robustly assemble full-length transcripts, including alternative splicing isoforms. In contrast to previous approaches, these two methods first map reads to the genome using software that takes possible splice junctions into account, thereby making assembly more manageable. Then, they apply graph-based algorithms to determine1, 2 and quantify1 the most likely splice isoforms. The algorithms were applied to mammalian transcriptomes to follow global patterns of splicing during a developmental time course1 and to identify novel, spliced, long, noncoding RNAs that had not been annotated by existing methods2.
- Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L. (2010) Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol 28(5), 511-15. [abstract]
- Guttman M, Garber M, Levin JZ, Donaghey J, Robinson J, Adiconis X, Fan L, Koziol MJ, Gnirke A, Nusbaum C, Rinn JL, Lander ES, Regev A. (2010) Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Nat Biotechnol (5), 503-10. [abstract]
- Mak HC. (2011) Next-generation sequence analysis. Nature Biotechnology 29, 45-46. [article]