13 参考文献[References]
Li, B., Ruotti, V., Stewart, R. M., Thomson, J. A. & Dewey, C. N. RNA-Seq gene expression estimation with read mapping uncertainty. Bioinformatics (Oxford, England) 26, 493–500; 10.1093/bioinformatics/btp692 (2010). Grabherr, M. G. et al. Trinity: reconstructing a full-length transcriptome without a genome from RNA-Seq data. Nature biotechnology 29, 644–652; 10.1038/nbt.1883 (2011). Li, B. & Dewey, C. N. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC bioinformatics 12, 323; 10.1186/1471-2105-12-323 (2011). Henschel, R. et al. in Proceedings of the XSEDE12 Conference: Bridging from the eXtreme to the Campus and Beyond, edited by C. Stewart, C. J. A. Stewart, W. Froelichelich, K. Hunt & P. Blood (Association for Computing Machinery, New York, New York, 2012), p. 1. Stewart, C., Stewart, C. J. A., Froelichelich, W., Hunt, K. & Blood, P. (eds.). Proceedings of the XSEDE12 Conference: Bridging from the eXtreme to the Campus and Beyond. July 16-19, 2012, InterContinental Magnificent Mile, Chicago (Association for Computing Machinery, New York, New York, 2012). Haas, B. J. et al. De novo transcript sequence reconstruction from RNA-Seq: reference generation and analysis with Trinity. Nature protocols 8; 10.1038/nprot.2013.084 (2013). Li, B. et al. Evaluation of de novo transcriptome assemblies from RNA-Seq data. Genome biology 15, 553; 10.1186/s13059-014-0553-5 (2014). Huerta-Cepas, J. et al. Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper. Molecular biology and evolution 34, 2115–2122; 10.1093/molbev/msx148 (2017). Seppey, M., Manni, M. & Zdobnov, E. M. BUSCO: Assessing Genome Assembly and Annotation Completeness. Methods in molecular biology (Clifton, N.J.) 1962, 227–245; 10.1007/978-1-4939-9173-0_14 (2019).