1. Trinity

Trinity，本博客之前介绍了：Trinity的安装与使用

Citation: Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q, Chen Z, Mauceli E, Hacohen N, Gnirke A, Rhind N, di Palma F, Birren BW, Nusbaum C, Lindblad-Toh K, Friedman N, Regev A. Full-length transcriptome assembly from RNA-seq data without a reference genome. Nat Biotechnol. 2011 May 15;29(7):644-52. doi: 10.1038/nbt.1883. PubMed PMID: 21572440.

2. Oases

Oases是EMBL-EBI开发出来的，是一种使用short reads（such as Illumina, SOLiD, or 454）进行de novo转录组组装的软件。Oases是在velvet的基础上开发的，其运行需要安装Velvet。

Citation：M.H. Schulz, D.R. Zerbino, M. Vingron and Ewan Birney. Oases: Robust de novo RNA-seq assembly across the dynamic range of expression levels. Bioinformatics, 2012. DOI: 10.1093/bioinformatics/bts094.

上文献中写道：It was tested on human and mouse RNA-seq data and is shown to improve significantly on the transABySS and Trinity de novo transcriptome assemblers.

3. EBARDenovo

EBARDenovo, which stands for Extension, Bridging And Repeat-sensing Denovo. This software package (with patent pending) is free of charge for academic use only.

Citation：Hsueh-Ting Chu,William W. L. Hsiao,Jen-Chih Chen,Tze-Jung Yeh,Mong-Hsun Tsai,Han Lin,Yen-Wenn Liu,Sheng-An Lee,Chaur-Chin Chen,Theresa T. H. Tsao,and Cheng-Yan Kao。EBARDenovo: highly accurate de novo assembly of RNA-Seq with efficient chimera-detection Bioinformatics (2013) 29 (8): 1004-1010 first published online March 1, 2013 doi:10.1093/bioinformatics/btt092

上文献中写道：our algorithm is the most accurate among the examined programs, including de Bruijn graph assemblers, Trinity and Oases.

4. Trans-ABySS

Trans-ABySS: Analyze ABySS multi-k-assembled shotgun transcriptome data.

Trans-ABySS 1.4.4, Released Oct 09, 2012, Supports both transcriptome and genome assemblies. A more robust pipeline and improvement to the 3 analysis suites (fusions, indels, and splicing).
Citation:Robertson G,et al. De novo assembly and analysis of RNA-seq data. Nat. Methods 2010;7:909-912.