gene fusion tools

*통합분석 소프트웨어(20일 시험판)
http://www.avadis-ngs.com/

*프로그램 검색 사이트
http://seqanswers.com/wiki/Special:BrowseData/Bioinformatics%20application?Biological_domain=Fusion_transcripts


*ChimeraScan
https://code.google.com/p/chimerascan/
Maher CA, Kumar-Sinha C, Cao X, Kalyana-Sundaram S, Han B, Jing X, Sam L, Barrette T, Palanisamy N, Chinnaiyan AM. Transcriptome sequencing to detect gene fusions in cancer. Nature 458, 97-101 2009.

*deFuse: gene fusion discovery using RNA-Seq
http://compbio.bccrc.ca/software/defuse/
McPherson A, Hormozdiari F, Zayed A, Giuliany R, Ha G, Sun MG, Griffith M, Heravi Moussavi A, Senz J, Melnyk N, Pacheco M, Marra MA, Hirst M, Nielsen TO, Sahinalp SC, Huntsman D, Shah SP. deFuse: an algorithm for gene fusion discovery in tumor RNA-Seq data. PLoS Comput Biol, 2011.

*FusionHunter: identifying fusion transcripts using paired-end RNA-seq
http://bioen-compbio.bioen.illinois.edu/FusionHunter/
Li Y, Chien J, Smith DI, Ma J. FusionHunter: identifying fusion transcripts in cancer using paired-end RNA-seq. Bioinformatics, 27(12):1708-10, 2011.

*FusionMap  detecting fusion genes from next-generation sequencing data at base-pair resolution
http://www.omicsoft.com/fusionmap/
Ge H, Liu K, Juan T, Fang F, Newman M, Hoeck W. FusionMap: detecting fusion genes from next-generation sequencing data at base-pair resolution. Bioinformatics, 2011.

*FusionSeq: a modular framework for finding gene fusions by analyzing Paired-End RNA-Sequencing data
http://archive.gersteinlab.org/proj/rnaseq/fusionseq/
Sboner A, Habegger L, Pflueger D, Terry S, Chen DZ, Rozowsky JS, Tewari AK, Kitabayashi N, Moss BJ, Chee MS, Demichelis F, Rubin MA, Gerstein MB. FusionSeq: a modular framework for finding gene fusions by analyzing Paired-End RNA-Sequencing data. Genome Biol, 21 Oct. 2010.

*TopHat-Fusion : An algorithm for Discovery of Novel Fusion Transcripts
http://tophat.cbcb.umd.edu/fusion_index.html
Kim D and Salzberg SL. TopHat-Fusion: an algorithm for discovery of novel fusion transcripts. Genome Biology, 2011.

*Trans-ABySS : Analyze ABySS multi-k-assembled shotgun transcriptome data.
http://www.bcgsc.ca/platform/bioinfo/software/trans-abyss
Robertson G, Schein J, Chiu R, Corbett R, Field M, Jackman SD, Mungall K, Lee S, Okada HM, Qian JQ, Griffith M, Raymond A, Thiessen N, Cezard T, Butterfield YS, Newsome R, Chan SK, She R, Varhol R, Kamoh B, Prabhu AL, Tam A, Zhao Y, Moore RA, Hirst M, Marra MA, Jones SJ, Hoodless PA, Birol I. De novo assembly and analysis of RNA-seq data. Nature Methods, 2011.