Ozsolak, F. & Milos, P. M. RNA sequencing: advances, challenges and opportunities. Nature Rev. Genet.12, 87–98 (2011). This Review provides a good, up-to-date summary of the RNA-seq experimental protocol and its usefulness in addressing important biological questions. ArticleCASPubMed Google Scholar
Wang, Z., Gerstein, M. & Snyder, M. RNA-seq: a revolutionary tool for transcriptomics. Nature Rev. Genet.10, 57–63 (2009). ArticleCASPubMed Google Scholar
Marguerat, S. & Bahler, J. RNA-seq: from technology to biology. Cell. Mol. Life Sci.67, 569–579 (2010). ArticleCASPubMed Google Scholar
Wilhelm, B. T. & Landry, J. R. RNA-seq-quantitative measurement of expression through massively parallel RNA-sequencing. Methods48, 249–257 (2009). ArticleCASPubMed Google Scholar
Metzker, M. L. Sequencing technologies — the next generation. Nature Rev. Genet.11, 31–46 (2010). This Review provides a good introduction to NGS technologies and the analysis challenges that they pose. CASPubMed Google Scholar
Paszkiewicz, K. & Studholme, D. J. De novo assembly of short sequence reads. Brief. Bioinform.11, 457–472 (2010). ArticleCASPubMed Google Scholar
Miller, J. R., Koren, S. & Sutton, G. Assembly algorithms for next-generation sequencing data. Genomics95, 315–327 (2010). This paper provides a good introduction to the current algorithms used in next-generation genome assembly and the challenges posed by these approaches. ArticleCASPubMed Google Scholar
Makalowska, I., Lin, C. F. & Makalowski, W. Overlapping genes in vertebrate genomes. Comput. Biol. Chem.29, 1–12 (2005). ArticleCASPubMed Google Scholar
Johnson, Z. I. & Chisholm, S. W. Properties of overlapping genes are conserved across microbial genomes. Genome Res.14, 2268–2272 (2004). ArticleCASPubMedPubMed Central Google Scholar
Fukuda, Y., Washio, T. & Tomita, M. Comparative study of overlapping genes in the genomes of Mycoplasma genitalium and Mycoplasma pneumoniae. Nucleic Acids Res.27, 1847–1853 (1999). ArticleCASPubMedPubMed Central Google Scholar
Martin, J. et al. Rnnotator: an automated de novo transcriptome assembly pipeline from stranded RNA-seq reads. BMC Genomics11, 663 (2010). This paper describes the firstde novotranscriptome assembler to automate the use of several k-mers for assembly. It also provides a good overview of methods used for the pre- and post-processing ofde novotranscriptome assemblies. ArticleCASPubMedPubMed Central Google Scholar
Guttman, M. et al. Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Nature Biotech.28, 503–510 (2010). This paper introduces the Scripture algorithm, which was one of the first reference-based assemblers that effectively tackled the assembly of alternative isoforms using NGS data. ArticleCAS Google Scholar
Robertson, G. et al. De novo assembly and analysis of RNA-seq data. Nature Methods7, 909–912 (2010). ArticleCASPubMed Google Scholar
Surget-Groba, Y. & Montoya-Burgos, J. I. Optimization of de novo transcriptome assembly from next-generation sequencing data. Genome Res.20, 1432–1440 (2010). ArticleCASPubMedPubMed Central Google Scholar
Trapnell, C. et al. Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nature Biotech.28, 511–515 (2010). The Cufflinks algorithm is introduced in this paper, which, like the Scripture algorithm described in reference 16, was one of the first reference-based assemblers that effectively tackled the assembly of alternative isoforms using NGS data. ArticleCAS Google Scholar
Birol, I. et al. De novo transcriptome assembly with ABySS. Bioinformatics25, 2872–2877 (2009). ArticleCASPubMed Google Scholar
Crawford, J. E. et al. De novo transcriptome sequencing in Anopheles funestus using Illumina RNA-seq technology. PLoS ONE5, e14202 (2010). ArticleCASPubMedPubMed Central Google Scholar
Garg, R., Patel, R. K., Tyagi, A. K. & Jain, M. De novo assembly of chickpea transcriptome using short reads for gene discovery and marker identification. DNA Res.18, 53–63 (2011). ArticleCASPubMedPubMed Central Google Scholar
Yassour, M. et al. Ab initio construction of a eukaryotic transcriptome by massively parallel mRNA sequencing. Proc. Natl Acad. Sci. USA106, 3264–3269 (2009). ArticleCASPubMedPubMed Central Google Scholar
Adamidi, C. et al. De novo assembly and validation of planaria transcriptome by massive parallel sequencing and shotgun proteomics. Genome Res.21, 1193–1200 (2011). ArticleCASPubMedPubMed Central Google Scholar
Katz, Y., Wang, E. T., Airoldi, E. M. & Burge, C. B. Analysis and design of RNA sequencing experiments for identifying isoform regulation. Nature Methods7, 1009–1015 (2010). ArticleCASPubMedPubMed Central Google Scholar
Levin, J. Z. et al. Comprehensive comparative analysis of strand-specific RNA sequencing methods. Nature Methods7, 709–715 (2010). This paper provides an excellent comparison of different RNA-seq protocols and how they affect the quantification of expression levels. ArticleCASPubMedPubMed Central Google Scholar
He, S. et al. Validation of two ribosomal RNA removal methods for microbial metatranscriptomics. Nature Methods7, 807–812 (2010). ArticleCASPubMed Google Scholar
Chen, Z. & Duan, X. Ribosomal RNA depletion for massively parallel bacterial RNA-sequencing applications. Methods Mol. Biol.733, 93–103 (2011). ArticleCASPubMed Google Scholar
Christodoulou, D. C., Gorham, J. M., Herman, D. S. & Seidman, J. G. Construction of normalized RNA-seq libraries for next-generation sequencing using the crab duplex-specific nuclease. Curr. Protoc. Mol. Biol. 1 Apr 2011 (doi:10.1002/0471142727.mb0412s94).
Kozarewa, I. et al. Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G+C)-biased genomes. Nature Methods6, 291–295 (2009). ArticleCASPubMedPubMed Central Google Scholar
Sam, L. T. et al. A comparison of single molecule and amplification based sequencing of cancer transcriptomes. PLoS ONE6, e17305 (2011). ArticleCASPubMedPubMed Central Google Scholar
Chen, S. et al. De novo analysis of transcriptome dynamics in the migratory locust during the development of phase traits. PLoS ONE5, e15633 (2010). ArticleCASPubMedPubMed Central Google Scholar
Schwartz, T. S. et al. A garter snake transcriptome: pyrosequencing, de novo assembly, and sex-specific differences. BMC Genomics11, 694 (2010). ArticleCASPubMedPubMed Central Google Scholar
Dalloul, R. A. et al. Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis. PLoS Biol.8, e1000475 (2010). ArticlePubMedPubMed Central Google Scholar
Shi, H., Schmidt, B., Liu, W. & Muller-Wittig, W. A parallel algorithm for error correction in high-throughput short-read data on CUDA-enabled graphics hardware. J. Comput. Biol.17, 603–615 (2010). ArticleCASPubMed Google Scholar
Kelley, D. R., Schatz, M. C. & Salzberg, S. L. Quake: quality-aware detection and correction of sequencing errors. Genome Biol.11, R116 (2010). ArticleCASPubMedPubMed Central Google Scholar
Falgueras, J. et al. SeqTrim: a high-throughput pipeline for pre-processing any type of sequence read. BMC Bioinformatics11, 38 (2010). ArticlePubMedPubMed Central Google Scholar
Lassmann, T., Hayashizaki, Y. & Daub, C. O. TagDust—a program to eliminate artifacts from next generation sequencing data. Bioinformatics25, 2839–2840 (2009). ArticleCASPubMedPubMed Central Google Scholar
Trapnell, C., Pachter, L. & Salzberg, S. L. TopHat: discovering splice junctions with RNA-seq. Bioinformatics25, 1105–1111 (2009). CASPubMed CentralPubMed Google Scholar
Au, K. F., Jiang, H., Lin, L., Xing, Y. & Wong, W. H. Detection of splice junctions from paired-end RNA-seq data by SpliceMap. Nucleic Acids Res.38, 4570–4578 (2010). ArticleCASPubMedPubMed Central Google Scholar
Wang, K. et al. MapSplice: accurate mapping of RNA-seq reads for splice junction discovery. Nucleic Acids Res.38, e178 (2010). ArticlePubMedPubMed Central Google Scholar
Wu, T. D. & Nacu, S. Fast and SNP-tolerant detection of complex variants and splicing in short reads. Bioinformatics26, 873–881 (2010). ArticleCASPubMedPubMed Central Google Scholar
Mortazavi, A., Williams, B. A., McCue, K., Schaeffer, L. & Wold, B. Mapping and quantifying mammalian transcriptomes by RNA-seq. Nature Methods5, 621–628 (2008). ArticleCASPubMed Google Scholar
Perkins, T. T. et al. A strand-specific RNA-seq analysis of the transcriptome of the typhoid bacillus Salmonella typhi. PLoS Genet.5, e1000569 (2009). ArticlePubMedPubMed Central Google Scholar
Ozsolak, F. et al. Comprehensive polyadenylation site maps in yeast and human reveal pervasive alternative polyadenylation. Cell143, 1018–1029 (2010). ArticleCASPubMedPubMed Central Google Scholar
Salzberg, S. L. & Yorke, J. A. Beware of mis-assembled genomes. Bioinformatics21, 4320–4321 (2005). This study highlights the importance of having standardized metrics to assess the quality of NGS assemblies. ArticleCASPubMed Google Scholar
Kinsella, M., Harismendy, O., Nakano, M., Frazer, K. A. & Bafna, V. Sensitive gene fusion detection using ambiguously mapping RNA-seq read pairs. Bioinformatics27, 1068–1075 (2011). ArticleCASPubMedPubMed Central Google Scholar
Tomlins, S. A. et al. Distinct classes of chromosomal rearrangements create oncogenic ETS gene fusions in prostate cancer. Nature448, 595–599 (2007). ArticleCASPubMed Google Scholar
Pevzner, P. A., Tang, H. & Waterman, M. S. An Eulerian path approach to DNA fragment assembly. Proc. Natl Acad. Sci. USA98, 9748–9753 (2001). This paper introduces the idea of using a De Bruijn graph for the purposes of assembly. ArticleCASPubMedPubMed Central Google Scholar
Grabherr, M. G. et al. Full-length transcriptome assembly from RNA-seq data without a reference genome. Nature Biotech.29, 644–652 (2011). The Trinityde novoassembly program is introduced in this paper. This was the first NGS transcriptome assembly strategy not to rely on a genome assembler while also addressing the assembly of alternative isoforms. ArticleCAS Google Scholar
Burset, M., Seledtsov, I. A. & Solovyev, V. V. Analysis of canonical and non-canonical splice sites in mammalian genomes. Nucleic Acids Res.28, 4364–4375 (2000). ArticleCASPubMedPubMed Central Google Scholar
Jager, M. et al. Composite transcriptome assembly of RNA-seq data in a sheep model for delayed bone healing. BMC Genomics12, 158 (2011). ArticlePubMedPubMed Central Google Scholar
Cocquet, J., Chong, A., Zhang, G. & Veitia, R. A. Reverse transcriptase template switching and false alternative transcripts. Genomics88, 127–131 (2006). ArticleCASPubMed Google Scholar
Haas, B. J. & Zody, M. C. Advancing RNA-seq analysis. Nature Biotech.28, 421–423 (2010). ArticleCAS Google Scholar
Greninger, A. L. et al. A metagenomic analysis of pandemic influenza A (2009 H1N1) infection in patients from North America. PLoS ONE5, e13381 (2010). ArticlePubMedPubMed Central Google Scholar
Mizuno, H. et al. Massive parallel sequencing of mRNA in identification of unannotated salinity stress-inducible transcripts in rice (Oryza sativa L.). BMC Genomics11, 683 (2010). ArticleCASPubMedPubMed Central Google Scholar
Twine, N. A., Janitz, K., Wilkins, M. R. & Janitz, M. Whole transcriptome sequencing reveals gene expression and splicing differences in brain regions affected by Alzheimer's disease. PLoS ONE6, e16266 (2011). ArticleCASPubMedPubMed Central Google Scholar
Meader, S., Hillier, L. W., Locke, D., Ponting, C. P. & Lunter, G. Genome assembly quality: assessment and improvement using the neutral indel model. Genome Res.20, 675–84 (2010). ArticleCASPubMedPubMed Central Google Scholar
Schaefer, B. C. Revolutions in rapid amplification of cDNA ends: new strategies for polymerase chain reaction cloning of full-length cDNA ends. Anal. Biochem.227, 255–273 (1995). ArticleCASPubMed Google Scholar
Taylor, R. C. An overview of the Hadoop/MapReduce/HBase framework and its current applications in bioinformatics. BMC Bioinformatics11 (Suppl. 12), S1 (2010). ArticlePubMedPubMed Central Google Scholar
Eid, J. et al. Real-time DNA sequencing from single polymerase molecules. Science323, 133–138 (2009). ArticleCASPubMed Google Scholar