三代全长转录本在辅助基因注释，可变剪接分析，融合基因检测方面可以说大显身手，下面小编列了几个工具及对应的下载地址，供大家参考。大家有好的最新的工具欢迎留言补充！
1. 可变剪接鉴定（3个工具）
1)网址：https://github.com/liuxiaoxian/IsoSeq_AS_de_novo
Liu X, Mei W, Soltis P S, et al. Detecting Alternatively Spliced Transcript Isoforms from Single‐Molecule Long‐Read Sequences without a Reference Genome[J]. Molecular Ecology Resources, 2017.
2)网址：http://splicegrapher.sourceforge.net/
Rogers M F, Thomas J, Reddy A S N, et al. SpliceGrapher: detecting patterns of alternative splicing from RNA-Seq data in the context of gene models and EST data[J]. Genome biology, 2012, 13(1): R4.
3)网址：https://sourceforge.net/projects/cash-program/
Wu W, Zong J, Wei N, et al. CASH: a constructing comprehensive splice site method for detecting alternative splicing events[J]. Briefings in Bioinformatics, 2017: bbx034.
2. 多平台结合分析高基因密度基因组
网址：https://github.com/flemingtonlab/public
O’Grady T, Wang X, Höner Zu Bentrup K, Baddoo M, Concha M, Flemington EK. Global transcript structure resolution of high gene density genomes through multi-platform data integration. Nucleic Acids Res. 2016 Jul 12; PMID: 27407110.
3. 全长转录本分析流程TAPIS
网址：https://bitbucket.org/comp_bio/tapis
Abdel-Ghany S E, Hamilton M, Jacobi J L, et al. A survey of the sorghum transcriptome using single-molecule long reads[J]. Nature communications, 2016, 7.
4. 全长转录组浏览器
网址：https://github.com/goeckslab/isoseq-browser
Hu J, Uapinyoying P, Goecks J. Interactive analysis of Long-read RNA isoforms with Iso-Seq Browser[J]. bioRxiv, 2017: 102905.
5.全长转录组测序新转录结构发现注释工具
网址：https://bitbucket.org/ConesaLab/sqanti
Tardaguila M, de la Fuente L, Marti C, et al. SQANTI: extensive characterization of long read transcript sequences for quality control in full-length transcriptome identification and quantification[J]. bioRxiv, 2017: 118083.
6.全长转录组Iso-Seq和RNA-Seq集合进行无参考转录组分析
Ning G, Cheng X, Luo P, et al. Hybrid sequencing and map finding (HySeMaFi): optional strategies for extensively deciphering gene splicing and expression in organisms without reference genome[J]. Scientific Reports, 2017, 7.
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