전사체 어셈블리 가속화를 위한 K-mer 기반 RNA-seq 데이터 분산 방법

키워드

참고문헌 (20)

1. Elaine R. Mardis, "The impact of next-generation sequencing technology on genetics", Trends in Genetics, 24(3), pp.133~141 (2008), Elsevier BV[DOI]
2. Robert Henschel, "Trinity RNA-Seq assembler performance optimization", Proceedings of the 1st Conference of the Extreme Science and Engineering Discovery Environment:Bridging from the eXtreme to the campus and beyond (XSEDE’12), pp.1~8 (2012), Association for Computing Machinery
3. Hölzer, Martin, "De novo transcriptome assembly: A comprehensive cross-species comparison of short-read RNA-Seq assemblers", GigaScience, 8 (2019)[DOI]
4. Goswami, Sayan, "Gpu-accelerated large-scale genome assembly", 2018 IEEE International Parallel and Distributed Processing Symposium (IPDPS) (2018), IEEE
5. Varma, B. Sharat Chandra, "FAssem: FPGA based acceleration of de novo genome assembly", 2013 IEEE 21st Annual International Symposium on Field-Programmable Custom Computing Machines, pp.173~176 (2013)
6. Ellis, Marquita, "diBELLA: Distributed long read to long read alignment", Proceedings of the 48th International Conference on Parallel Processingm, (70), pp.1~11 (2019)
7. Henschel, Robert, "Trinity RNA-Seq assembler performance optimization", Proceedings of the 1st Conference of the Extreme Science and Engineering Discovery Environment: Bridging from the eXtreme to the campus and beyond (2012)
8. Brian J Haas, "De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis", Nature Protocols, 8(8), pp.1494~1512 (2013), Springer Science and Business Media LLC[DOI]
9. Chang Sik Kim, "K-mer clustering algorithm using a MapReduce framework: application to the parallelization of the Inchworm module of Trinity", BMC Bioinformatics, 18(1) (2017), Springer Science and Business Media LLC[DOI]
10. Qiong-Yi Zhao, "Optimizing de novo transcriptome assembly from short-read RNA-Seq data: a comparative study", BMC Bioinformatics, 12(Suppl 14), pp.S2~ (2011), Springer Science and Business Media LLC[DOI]
11. Wagner, Michael, "Perform ance Optimization for the Trinity RNA-Seq Assembler", Tools for High Performance Computing 2015, pp.29~40 (2016)
12. D. Yan, "Scalable De Novo Genome Assembly Using Pregel", 2018 IEEE 34th International Conference on Data Engineering (ICDE), pp.1216~1219 (2018)
13. Lamesch P, "The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools", Nucleic Acids Res, pp.D1202~D1210 (2012)[DOI]
14. "NCBI SRA database(Arabidopsis Thaliana)"[URL]
15. Nancy Manchanda, "GenomeQC: a quality assessment tool for genome assemblies and gene structure annotations", BMC Genomics, 21(1) (2020), Springer Science and Business Media LLC[DOI]
16. Ajay Kumar Saw, "Alignment-free method for DNA sequence clustering using Fuzzy integral similarity", Scientific Reports, 9(1) (2019), Springer Science and Business Media LLC[DOI]
17. Renesh Bedre, "GenFam: A web application and database for gene family‐based classification and functional enrichment analysis", Plant Direct, 3(12), pp.1~7 (2019), Wiley[DOI]
18. Tinashe G. Chabikwa, "De novo transcriptome assembly and annotation for gene discovery in avocado, macadamia and mango", Scientific Data, 7(1) (2020), Springer Science and Business Media LLC[DOI]
19. Seokjun Seo, "DeepFam:deep learning based alignment-free method for protein family modeling and prediction", Bioinformatics, 34(13), pp.254~262 (2018)[DOI]
20. Weizhong Li, "Ultrafast clustering algorithms for metagenomic sequence analysis", Bioinformatics, 13(6), pp.656~668 (2012)[DOI]

관련 논문AI추천