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De novo assembly of transcriptome from next-generation sequencing data

Xuan Li, Yimeng Kong, Qiong-Yi Zhao, Yuan-Yuan Li, Pei Hao
2016 Quantitative Biology  
Future direction points to the combination of NGS and third generation sequencing technology that would greatly enhance the power of de novo transcriptomics study.  ...  In the current review, we illustrate the grand strategy in applying De Bruijn Graph (DBG) approach in de novo transcriptome assembly.  ...  ACKNOWLEDGEMENTS COMPLIANCE WITH ETHICS GUIDELINES The authors Xuan Li, Yimeng Kong, Qiong-Yi Zhao, Yuan-Yuan Li and Pei Hao declare they have no conflict of interests.  ... 
doi:10.1007/s40484-016-0069-y fatcat:zo2zm2adifdaddnfth6aks5hua

Optimizing de novo transcriptome assembly from short-read RNA-Seq data: a comparative study

Qiong-Yi Zhao, Yi Wang, Yi-Meng Kong, Da Luo, Xuan Li, Pei Hao
2011 BMC Bioinformatics  
ABySS showed some good balance between resource usage and quality of assemblies.  ...  Conclusions: Our work compared the performance of publicly available transcriptome assemblers, and analyzed important factors affecting de novo assembly.  ...  Acknowledgements The authors would like to thank Zhi-Yong Shen for his assistance on computation support, and Lei Zhang and Fei He for their helpful discussion.  ... 
doi:10.1186/1471-2105-12-s14-s2 pmid:22373417 pmcid:PMC3287467 fatcat:f2svmdps6jazxb37zbn6oyy7pq

Establishing evidenced-based best practice for the de novo assembly and evaluation of transcriptomes from non-model organisms [article]

Matthew D MacManes
2015 bioRxiv   pre-print
Using reference and non-reference based evaluative methods, I propose a set of guidelines that aim to standardize and facilitate the process of transcriptome assembly.  ...  For many, these studies begin with a de novo transcriptome assembly, which is a technically complicated process involving several discrete steps.  ...  , on the production 47 of accurate transcriptome resources.  ... 
doi:10.1101/035642 fatcat:v223xyx64ff3pe7mxbumbsm46q

Pseudo-Reference-Based Assembly of Vertebrate Transcriptomes

Kyoungwoo Nam, Heesu Jeong, Jin-Wu Nam
2016 Genes  
Here, we developed a pseudo-reference-based assembly (PRA) that reconstructs a transcriptome based on a linear regression function of the optimized mapping parameters and genetic distances of the closest  ...  High-throughput RNA sequencing (RNA-seq) provides a comprehensive picture of the transcriptome, including the identity, structure, quantity, and variability of expressed transcripts in cells, through the  ...  Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/genes7030010 pmid:26927182 pmcid:PMC4808791 fatcat:sceofzjfkbdotjowfjze6ajom4

What are the most influencing factors in reconstructing a reliable transcriptome assembly? [article]

Noushin Ghaffari, Jordi Abante, Raminder Singh, Philip D Blood, Lenore Pipes, Christopher Mason, Charles D Johnson
2017 bioRxiv   pre-print
Thus, once a certain coverage is attained, the quality of the assembly is mainly dependent on the base-calling accuracy of the input sequencing reads; and it is important to avoid saturating the assembler  ...  Our results indicate that the quality of the library construction significantly impacts the quality of the assembly.  ...  the National Institutes of Health (R21AI129851).  ... 
doi:10.1101/220269 fatcat:25xigzzc25aebmm2gzcwdzd7wu

Optimizing and benchmarking de novo transcriptome sequencing: from library preparation to assembly evaluation

Yuichiro Hara, Kaori Tatsumi, Michio Yoshida, Eriko Kajikawa, Hiroshi Kiyonari, Shigehiro Kuraku
2015 BMC Genomics  
In order to evaluate the completeness of transcriptome assemblies, we prepared a reference gene set consisting of vertebrate one-to-one orthologs.  ...  The output reads were assembled de novo for reconstructing transcript sequences.  ...  Our gratitude extends to Munazah Andrabi and Sean Keeley for critical reading of the manuscript.  ... 
doi:10.1186/s12864-015-2007-1 pmid:26581708 pmcid:PMC4652379 fatcat:as3c2wm4nzakndly2qhgotalk4

Challenges and advances for transcriptome assembly in non-model species

Arnaud Ungaro, Nicolas Pech, Jean-François Martin, R. J. Scott McCairns, Jean-Philippe Mévy, Rémi Chappaz, André Gilles, Marinus F. W. te Pas
2017 PLoS ONE  
OPEN ACCESS Citation: Ungaro A, Pech N, Martin J-F, McCairns RJS, Mévy J-P, Chappaz R, et al. (2017) Challenges and advances for transcriptome assembly in non-model species.  ...  PLoS ONE 12(9): e0185020.  ...  Acknowledgments We are particularly grateful to Bernard Barascud for his invaluable contributions to the common garden experiments.  ... 
doi:10.1371/journal.pone.0185020 pmid:28931057 pmcid:PMC5607178 fatcat:zk5mdw6bkvbg7fkmnxp3z7tqja

The influence of trematode parasite burden on gene expression in a mammalian host

Bhagya K. Wijayawardena, Dennis J. Minchella, J. Andrew DeWoody
2016 BMC Genomics  
We used two different methodologies (i.e. de novo and reference guided) to evaluate the influence of parasite sequences on host transcriptome assembly.  ...  To identify global changes in host gene expression related to parasite infection, we sequenced, assembled, and annotated the liver transcriptomes of Balb/cj mice infected with the trematode parasite Schistosoma  ...  Acknowledgements We thank members of the DeWoody and Minchella labs for their feedback on an earlier version of the manuscript.  ... 
doi:10.1186/s12864-016-2950-5 pmid:27514777 pmcid:PMC4982272 fatcat:fjhxndiiaja5zeign64nhuw73i

TransFlow: a modular framework for assembling and assessing accurate de novo transcriptomes in non-model organisms

Pedro Seoane, Marina Espigares, Rosario Carmona, Álvaro Polonio, Julia Quintana, Enrico Cretazzo, Josefina Bota, Alejandro Pérez-García, Juan de Dios Alché, Luis Gómez, M. Gonzalo Claros
2018 BMC Bioinformatics  
The advances in high-throughput sequencing technologies are allowing more and more de novo assembling of transcriptomes from many new organisms.  ...  Workflows and pipelines are becoming an absolute requirement for such a purpose, but the issue of assembling evaluation for de novo transcriptomes in organisms lacking a sequenced genome remains unsolved  ...  Acknowledgements This work would not have been possible without the computer resources and the technical support provided by the Plataforma Andaluza de Bioinformática of the University of Málaga.  ... 
doi:10.1186/s12859-018-2384-y fatcat:fctwmkroujgutll37ifm3wfhku

A consensus approach to vertebrate de novo transcriptome assembly from RNA-seq data: assembly of the duck (Anas platyrhynchos) transcriptome

Joanna Moreton, Stephen P. Dunham, Richard D. Emes
2014 Frontiers in Genetics  
RESULTS GENERATION OF DIFFERENT DE NOVO TRANSCRIPT ASSEMBLIES De novo transcriptomes were first generated using all of the 277 million quality filtered reads then on a random sub-sample of 30 million  ...  The results here suggest that a robust de novo transcriptome can be generated, with limited computational resources using (1) a random sub-sample of the reads; (2) three different assembly tools; (3) merging  ... 
doi:10.3389/fgene.2014.00190 pmid:25009556 pmcid:PMC4070175 fatcat:netimdhxjbhfdgjsvhryaitrwq

The Oyster River Protocol: A Multi Assembler and Kmer Approach For de novo Transcriptome Assembly [article]

Matthew D MacManes
2017 bioRxiv   pre-print
For many, these studies begin with a de novo transcriptome assembly, which is a technically complicated process involving several discrete steps.  ...  thereby bypassing the shortcomings of any one approach.  ...  Titus Brown, Brian Haas and many others. More generally, the work and its presentation has been influenced by supporters of the Open Access and Open Science movements.  ... 
doi:10.1101/177253 fatcat:znaljjjuurcd7coaivm7mrocna

Challenges and advances for transcriptome assembly in non-model species [article]

Arnaud Ungaro, Nicolas Pech, Jean-Francois Martin, Scott RJ McCairns, Jean-Philippe Mevy, Remi Chappaz, Andre Gilles
2016 bioRxiv   pre-print
Analyses of high-throughput transcriptome sequences of non-model organisms are based on two main approaches: de novo assembly and genome-guided assembly using mapping to assign reads prior to assembly.  ...  We also compare the performances of de novo assembly alone vs in combination with a transcriptome-guided assembly based on blastn via simulation and empirically, using data from a cyprinid fish species  ...  S9 Figure : Biological processes of the identified genes. S10 Text : Computing resources and computation time.  ... 
doi:10.1101/084145 fatcat:nvfumnimpzfy5cmwv23dgvq76a

A comprehensive comparison of RNA-Seq-based transcriptome analysis from reads to differential gene expression and cross-comparison with microarrays: a case study in Saccharomyces cerevisiae

Intawat Nookaew, Marta Papini, Natapol Pornputtapong, Gionata Scalcinati, Linn Fagerberg, Matthias Uhlén, Jens Nielsen
2012 Nucleic Acids Research  
and de novo assembly approach.  ...  Here, we asses the influence of genetic variation on the estimation of gene expression level using three different aligners for read-mapping (Gsnap, Stampy and TopHat) on S288c genome, the capabilities  ...  The computational analyses were performed on resources provided by the Swedish National Infrastructure for Computing (SNIC) at C3SE. Gothenburg Bioinformatics Network (GOTBIN).  ... 
doi:10.1093/nar/gks804 pmid:22965124 pmcid:PMC3488244 fatcat:qlmthnmrz5gvllnqrk5pzbrzsq

Informedkmer selection forde novotranscriptome assembly

Dilip A. Durai, Marcel H. Schulz
2016 Bioinformatics  
Most de novo transcriptome assemblers use the de Bruijn graph (DBG) as the underlying data structure.  ...  The quality of the assemblies produced by such assemblers is highly influenced by the exact word length k. As such no single kmer value leads to optimal results.  ...  Funding This work was supported by the Cluster of Excellence on Multimodal Computing and Interaction (EXC284) of the German National Science Foundation (DFG).  ... 
doi:10.1093/bioinformatics/btw217 pmid:27153653 pmcid:PMC4892416 fatcat:72ws5ee4jnfsjakse565ojd6su

Transcriptome analysis of northern elephant seal (Mirounga angustirostris) muscle tissue provides a novel molecular resource and physiological insights

Jane I Khudyakov, Likit Preeyanon, Cory D Champagne, Rudy M Ortiz, Daniel E Crocker
2015 BMC Genomics  
Conclusions: We present the first reference sequence for Mirounga angustirostris produced by RNA sequencing of muscle tissue and cloud-based de novo transcriptome assembly.  ...  De novo assembly generated 164,966 contigs and a total of 522,699 transcripts, of which 68.70% were annotated using mouse, human, and domestic dog reference protein sequences.  ...  Sheneman for development and assistance implementing the Eel Pond mRNAseq protocol. We thank C. T. Brown for insightful comments on data analysis and the manuscript.  ... 
doi:10.1186/s12864-015-1253-6 pmid:25758323 pmcid:PMC4328371 fatcat:uahqmtzrajhpniaa5wejrxlu24
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