References
Abate F, Acquaviva A, Paciello G, et al. (2012) Bellerophontes: an RNA‐Seq data analysis framework for chimeric transcripts discovery based on accurate fusion model. Bioinformatics 28: 2114–2121.
Abel HJ, Al‐Kateb H, Cottrell CE, et al. (2014) Detection of gene rearrangements in targeted clinical next‐generation sequencing. Journal of Molecular Diagnostics 16: 405–417.
Ameur A, Wetterbom A, Feuk L and Gyllensten U (2010) Global and unbiased detection of splice junctions from RNA‐seq data. Genome Biology 11: R34.
Asmann YW, Hossain A, Necela BM, et al. (2011) A novel bioinformatics pipeline for identification and characterization of fusion transcripts in breast cancer and normal cell lines. Nucleic Acids Research 39: e100.
Au KF, Jiang H, Lin L, Xing Y and Wong WH (2010) Detection of splice junctions from paired‐end RNA‐seq data by SpliceMap. Nucleic Acids Research 38: 4570–4578.
Benelli M, Pescucci C, Marseglia G, et al. (2012) Discovering chimeric transcripts in paired‐end RNA‐seq data by using EricScript. Bioinformatics 28: 3232–3239.
Bruno AE, Miecznikowski JC, Qin M, Wang J and Liu S (2013) FUSIM: a software tool for simulating fusion transcripts. BMC Bioinformatics 14: 13.
Bryant DW Jr Shen R, Priest HD, Wong WK and Mockler TC (2010) Supersplat – spliced RNA‐seq alignment. Bioinformatics 26: 1500–1505.
Chen K, Wallis JW, Kandoth C, et al. (2012) BreakFusion: targeted assembly‐based identification of gene fusions in whole transcriptome paired‐end sequencing data. Bioinformatics 28: 1923–1924.
Chen K, Wallis JW, McLellan MD, et al. (2009) BreakDancer: an algorithm for high‐resolution mapping of genomic structural variation. Nature Methods 6: 677–681.
Clement NL, Snell Q, Clement MJ, et al. (2010) The GNUMAP algorithm: unbiased probabilistic mapping of oligonucleotides from next‐generation sequencing. Bioinformatics 26: 38–45.
Cloonan N, Xu Q, Faulkner GJ, et al. (2009) RNA‐MATE: a recursive mapping strategy for high‐throughput RNA‐sequencing data. Bioinformatics 25: 2615–2616.
Dimon MT, Sorber K and DeRisi JL (2010) HMMSplicer: a tool for efficient and sensitive discovery of known and novel splice junctions in RNA‐Seq data. PLoS One 5: e13875.
Dobin A, Davis CA, Schlesinger F, et al. (2013) STAR: ultrafast universal RNA‐seq aligner. Bioinformatics 29: 15–21.
Francis RW, Thompson‐Wicking K, Carter KW, et al. (2012) FusionFinder: a software tool to identify expressed gene fusion candidates from RNA‐Seq data. PLoS One 7: e39987.
Ge H, Liu K, Juan T, et al. (2011) FusionMap: detecting fusion genes from next‐generation sequencing data at base‐pair resolution. Bioinformatics 27: 1922–1928.
Gotoh O (1982) An improved algorithm for matching biological sequences. Journal of Molecular Biology 162: 705–708.
Grant GR, Farkas MH, Pizarro AD, et al. (2011) Comparative analysis of RNA‐Seq alignment algorithms and the RNA‐Seq unified mapper (RUM). Bioinformatics 27: 2518–2528.
Homer N, Merriman B and Nelson SF (2009) BFAST: an alignment tool for large scale genome resequencing. PLoS One 4: e7767.
Hsu F, Kent WJ, Clawson H, et al. (2006) The UCSC known genes. Bioinformatics 22: 1036–1046.
Huang S, Zhang J, Li R, et al. (2011) SOAPsplice: genome‐wide ab initio detection of splice junctions from RNA‐seq data. Frontiers in Genetics 2: 46.
Iyer MK, Chinnaiyan AM and Maher CA (2011) ChimeraScan: a tool for identifying chimeric transcription in sequencing data. Bioinformatics 27: 2903–2904.
Jean G, Kahles A, Sreedharan VT, De Bona F and Ratsch G (2010) RNA‐Seq read alignments with PALMapper. Current Protocols in Bioinformatics Chapter 11, Unit 11 6.
Jia W, Qiu K, He M, et al. (2013) SOAPfuse: an algorithm for identifying fusion transcripts from paired‐end RNA‐Seq data. Genome Biology 14: R12.
Kangaspeska S, Hultsch S, Edgren H, et al. (2012) Reanalysis of RNA‐sequencing data reveals several additional fusion genes with multiple isoforms. PLoS One 7: e48745.
Kim D and Salzberg SL (2011) TopHat‐Fusion: an algorithm for discovery of novel fusion transcripts. Genome Biology 12: R72.
Kinsella M, Harismendy O, Nakano M, Frazer KA and Bafna V (2011) Sensitive gene fusion detection using ambiguously mapping RNA‐Seq read pairs. Bioinformatics 27: 1068–1075.
Korbel JO, Abyzov A, Mu XJ, et al. (2009) PEMer: a computational framework with simulation‐based error models for inferring genomic structural variants from massive paired‐end sequencing data. Genome Biology 10: R23.
Langmead B and Salzberg SL (2012) Fast gapped‐read alignment with Bowtie 2. Nature Methods 9: 357–359.
Langmead B, Trapnell C, Pop M and Salzberg SL (2009) Ultrafast and memory‐efficient alignment of short DNA sequences to the human genome. Genome Biology 10: R25.
Lee WP, Stromberg MP, Ward A, et al. (2014) MOSAIK: a hash‐based algorithm for accurate next‐generation sequencing short‐read mapping. PLoS One 9: e90581.
Li H and Durbin R (2009) Fast and accurate short read alignment with Burrows‐Wheeler transform. Bioinformatics 25: 1754–1760.
Li H, Ruan J and Durbin R (2008) Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Research 18: 1851–1858.
Li R, Yu C, Li Y, et al. (2009) SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics 25: 1966–1967.
Li Y, Chien J, Smith DI and Ma J (2011) FusionHunter: identifying fusion transcripts in cancer using paired‐end RNA‐seq. Bioinformatics 27: 1708–1710.
Liao Y, Smyth GK and Shi W (2013) The Subread aligner: fast, accurate and scalable read mapping by seed‐and‐vote. Nucleic Acids Research 41: e108.
Lin H, Zhang Z, Zhang MQ, Ma B and Li M (2008) ZOOM! Zillions of oligos mapped. Bioinformatics 24: 2431–2437.
Liu C, Ma J, Chang CJ and Zhou X (2013) FusionQ: a novel approach for gene fusion detection and quantification from paired‐end RNA‐Seq. BMC Bioinformatics 14: 193.
Lou SK, Ni B, Lo LY, et al. (2011) ABMapper: a suffix array‐based tool for multi‐location searching and splice‐junction mapping. Bioinformatics 27: 421–422.
Lunter G and Goodson M (2011) Stampy: a statistical algorithm for sensitive and fast mapping of Illumina sequence reads. Genome Research 21: 936–939.
McPherson A, Hormozdiari F, Zayed A, et al. (2011a) deFuse: an algorithm for gene fusion discovery in tumor RNA‐Seq data. PLOS Computational Biology 7: e1001138.
McPherson A, Wu C, Hajirasouliha I, et al. (2011b) Comrad: detection of expressed rearrangements by integrated analysis of RNA‐Seq and low coverage genome sequence data. Bioinformatics 27: 1481–1488.
McPherson A, Wu C, Wyatt AW, et al. (2012) nFuse: discovery of complex genomic rearrangements in cancer using high‐throughput sequencing. Genome Research 22: 2250–2261.
Philippe N, Salson M, Commes T and Rivals E (2013) CRAC: an integrated approach to the analysis of RNA‐seq reads. Genome Biology 14: R30.
Piazza R, Pirola A, Spinelli R, et al. (2012) FusionAnalyser: a new graphical, event‐driven tool for fusion rearrangements discovery. Nucleic Acids Research 40: e123.
Pruitt KD, Tatusova T and Maglott DR (2007) NCBI reference sequences (RefSeq): a curated non‐redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Research 35: D61–D65.
Robertson G, Schein J, Chiu R, et al. (2010) De novo assembly and analysis of RNA‐seq data. Nature Methods 7: 909–912.
Rumble SM, Lacroute P, Dalca AV, et al. (2009) SHRiMP: accurate mapping of short color‐space reads. PLoS Computational Biology 5: e1000386.
Sboner A, Habegger L, Pflueger D, et al. (2010) FusionSeq: a modular framework for finding gene fusions by analyzing paired‐end RNA‐sequencing data. Genome Biology 11: R104.
Sedlazeck FJ, Rescheneder P and von Haeseler A (2013) NextGenMap: fast and accurate read mapping in highly polymorphic genomes. Bioinformatics 29: 2790–2791.
Smith TF and Waterman MS (1981) Identification of common molecular subsequences. Journal of Molecular Biology 147: 195–197.
Sun R, Love MI, Zemojtel T, et al. (2012) Breakpointer: using local mapping artifacts to support sequence breakpoint discovery from single‐end reads. Bioinformatics 28: 1024–1025.
Trapnell C, Pachter L and Salzberg SL (2009) TopHat: discovering splice junctions with RNA‐Seq. Bioinformatics 25: 1105–1111.
Wang J, Mullighan CG, Easton J, et al. (2011) CREST maps somatic structural variation in cancer genomes with base‐pair resolution. Nature Methods 8: 652–654.
Wang K, Singh D, Zeng Z, et al. (2010) MapSplice: accurate mapping of RNA‐seq reads for splice junction discovery. Nucleic Acids Research 38: e178.
Wu J, Zhang W, Huang S, et al. (2013) SOAPfusion: a robust and effective computational fusion discovery tool for RNA‐seq reads. Bioinformatics 29: 2971–2978.
Ye K, Schulz MH, Long Q, Apweiler R and Ning Z (2009) Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired‐end short reads. Bioinformatics 25: 2865–2871.
Zeitouni B, Boeva V, Janoueix‐Lerosey I, et al. (2010) SVDetect: a tool to identify genomic structural variations from paired‐end and mate‐pair sequencing data. Bioinformatics 26: 1895–1896.
Further Reading
Edwards PA (2010) Fusion genes and chromosome translocations in the common epithelial cancers. Journal of Pathology 220: 244–254.
Medves S and Demoulin JB (2012) Tyrosine kinase gene fusions in cancer: translating mechanisms into targeted therapies. Journal of Cellular and Molecular Medicine 16: 237–248.