Seqdev: an algorithm for constructing genetic elements using comparative assembly
Tasnim Rahman,Hasnain Heickal,Shamira Tabrejee,Miraj Kobad Chowdhury,Sheikh Muhammad Sarwar,Mohammad Shoyaib +5 more
TL;DR: This article was published in Plant Tissue Culture and Biotechnology [© 2016, Bangladesh Association for plant Tissue] and the definite version is available at: http://dx.doi.org/10.3329/ptcb.v26i1.29772.
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Abstract: This article was published in Plant Tissue Culture and Biotechnology [© 2016, Bangladesh Association for Plant Tissue] and the definite version is available at: http://dx.doi.org/10.3329/ptcb.v26i1.29772. The Journal's website is at: http://www.banglajol.info/index.php/PTCB/article/view/29772
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References
The MaSuRCA genome assembler
Aleksey V. Zimin,Guillaume Marçais,Daniela Puiu,Michael Roberts,Steven L. Salzberg,James A. Yorke +5 more
TL;DR: A new hybrid approach that has the computational efficiency of de Bruijn graph methods and the flexibility of overlap-based assembly strategies, and which allows variable read lengths while tolerating a significant level of sequencing error is described.
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Assembly algorithms for next-generation sequencing data.
TL;DR: This review summarizes and compares the published descriptions of packages named SSAKE, SHARCGS, VCAKE, Newbler, Celera Assembler, Euler, Velvet, ABySS, AllPaths, and SOAPdenovo to compare the two standard methods known as the de Bruijn graph approach and the overlap/layout/consensus approach to assembly.
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SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads
Yinlong Xie,Yinlong Xie,Gengxiong Wu,Jingbo Tang,Ruibang Luo,Jordan Patterson,Shanlin Liu,Weihua Huang,Guangzhu He,Shengchang Gu,Shengkang Li,Xin Zhou,Tak-Wah Lam,Yingrui Li,Xun Xu,Gane Ka-Shu Wong,Jun Wang +16 more
TL;DR: The conclusion is that SOAPdenovo-Trans provides higher contiguity, lower redundancy and faster execution, compared with two other popular transcriptome assemblers.
Aggressive assembly of pyrosequencing reads with mates
Jason R. Miller,Arthur L. Delcher,Sergey Koren,Eli Venter,Brian P. Walenz,Anushka Brownley,Justin Johnson,Kelvin Li,Clark M. Mobarry,Granger G. Sutton +9 more
TL;DR: The revised pipeline called CABOG (Celera Assembler with the Best Overlap Graph) is robust to homopolymer run length uncertainty, high read coverage and heterogeneous read lengths, and in tests on four genomes, it generated the longest contigs among all assemblers tested.
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•Posted Content
SOAPdenovo-Trans: De novo transcriptome assembly with short RNA-Seq reads
Yinlong Xie,Yinlong Xie,Gengxiong Wu,Jingbo Tang,Ruibang Luo,Jordan Patterson,Shanlin Liu,Weihua Huang,Guangzhu He,Shengchang Gu,Shengkang Li,Xin Zhou,Tak-Wah Lam,Yingrui Li,Xun Xu,Gane Ka-Shu Wong,Jun Wang +16 more
TL;DR: SOAPdenovo-Trans as mentioned in this paper is a de novo transcriptome assembler designed specifically for RNA-Seq that provides higher contiguity, lower redundancy, and faster execution.
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