Trinity<\/a>\uff0c\u672c\u535a\u5ba2\u4e4b\u524d\u4ecb\u7ecd\u4e86\uff1aTrinity\u7684\u5b89\u88c5\u4e0e\u4f7f\u7528<\/a><\/p>\n 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<\/a>. <\/p>\n Oases<\/a>\u662fEMBL-EBI\u5f00\u53d1\u51fa\u6765\u7684\uff0c\u662f\u4e00\u79cd\u4f7f\u7528short reads\uff08such as Illumina, SOLiD, or 454\uff09\u8fdb\u884cde novo\u8f6c\u5f55\u7ec4\u7ec4\u88c5\u7684\u8f6f\u4ef6\u3002Oases\u662f\u5728velvet\u7684\u57fa\u7840\u4e0a\u5f00\u53d1\u7684\uff0c\u5176\u8fd0\u884c\u9700\u8981\u5b89\u88c5Velvet\u3002<\/p>\n Citation\uff1aM.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.<\/a><\/p>\n \u4e0a\u6587\u732e\u4e2d\u5199\u9053\uff1aIt was tested on human and mouse RNA-seq data and is shown to improve significantly on the transABySS and Trinity de novo transcriptome assemblers. <\/p>\n EBARDenovo<\/a>, which stands for Extension, Bridging And Repeat-sensing Denovo. This software package (with patent pending) is free of charge for academic use only. <\/p>\n Citation\uff1aHsueh-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\u3002EBARDenovo: 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 <\/a><\/p>\n \u4e0a\u6587\u732e\u4e2d\u5199\u9053\uff1aour algorithm is the most accurate among the examined programs, including de Bruijn graph assemblers, Trinity and Oases. <\/p>\n Trans-ABySS<\/a>: Analyze ABySS multi-k-assembled shotgun transcriptome data.<\/p>\n 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). 1. Trinity Trinity\uff0c\u672c\u535a\u5ba2\u4e4b\u524d\u4ecb\u7ecd\u4e86\uff1aTrinity\u7684\u5b89\u88c5\u4e0e\u4f7f … \u7ee7\u7eed\u9605\u8bfb 2. Oases<\/h1>\n
3. EBARDenovo<\/h1>\n
4. Trans-ABySS<\/h1>\n
\nCitation:Robertson G,et al. De novo assembly and analysis of RNA-seq data. Nat. Methods 2010;7:909-912.<\/a><\/p>\n","protected":false},"excerpt":{"rendered":"