PanACoTA: A modular tool for massive microbial comparative genomics

作者: Amandine Perrin , Eduardo P.C. Rocha

DOI: 10.1101/2020.09.11.293472

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摘要: … genomic datasets puts a heavy burden on researchers, especially those that lack extensive training in bioinformatics… , to get the families common to a set of genomes, to align them, or to …

参考文章(57)
Kathryn E Holt, Heiman Wertheim, Ruth N Zadoks, Stephen Baker, Chris A Whitehouse, David Dance, Adam Jenney, Thomas R Connor, Li Yang Hsu, Juliëtte Severin, Sylvain Brisse, Hanwei Cao, Jonathan Wilksch, Claire Gorrie, Mark B Schultz, David J Edwards, Kinh Van Nguyen, Trung Vu Nguyen, Trinh Tuyet Dao, Martijn Mensink, Vien Le Minh, Nguyen Thi Khanh Nhu, Constance Schultsz, Kuntaman Kuntaman, Paul N Newton, Catrin E Moore, Richard A Strugnell, Nicholas R Thomson, None, Genomic analysis of diversity, population structure, virulence, and antimicrobial resistance in Klebsiella pneumoniae, an urgent threat to public health Proceedings of the National Academy of Sciences of the United States of America. ,vol. 112, pp. 201501049- ,(2015) , 10.1073/PNAS.1501049112
Morgan N. Price, Paramvir S. Dehal, Adam P. Arkin, FastTree 2--approximately maximum-likelihood trees for large alignments. PLOS ONE. ,vol. 5, ,(2010) , 10.1371/JOURNAL.PONE.0009490
Benjamin Buchfink, Chao Xie, Daniel H Huson, Fast and sensitive protein alignment using DIAMOND Nature Methods. ,vol. 12, pp. 59- 60 ,(2015) , 10.1038/NMETH.3176
Derrick E. Fouts, Lauren Brinkac, Erin Beck, Jason Inman, Granger Sutton, PanOCT: automated clustering of orthologs using conserved gene neighborhood for pan-genomic analysis of bacterial strains and closely related species Nucleic Acids Research. ,vol. 40, ,(2012) , 10.1093/NAR/GKS757
S Altschula, Warren Gisha, Webb Millerb, E Meyersc, D Lipmana, None, Basic Local Alignment Search Tool Journal of Molecular Biology. ,vol. 215, pp. 403- 410 ,(1990) , 10.1016/S0022-2836(05)80360-2
George Vernikos, Duccio Medini, David R Riley, Hervé Tettelin, Ten years of pan-genome analyses. Current Opinion in Microbiology. ,vol. 23, pp. 148- 154 ,(2015) , 10.1016/J.MIB.2014.11.016
Julie D. Thompson, Benjamin Linard, Odile Lecompte, Olivier Poch, A Comprehensive Benchmark Study of Multiple Sequence Alignment Methods: Current Challenges and Future Perspectives PLoS ONE. ,vol. 6, pp. e18093- 18093 ,(2011) , 10.1371/JOURNAL.PONE.0018093
T. Seemann, Prokka: Rapid Prokaryotic Genome Annotation Bioinformatics. ,vol. 30, pp. 2068- 2069 ,(2014) , 10.1093/BIOINFORMATICS/BTU153
P. Jones, D. Binns, H.-Y. Chang, M. Fraser, W. Li, C. McAnulla, H. McWilliam, J. Maslen, A. Mitchell, G. Nuka, S. Pesseat, A. F. Quinn, A. Sangrador-Vegas, M. Scheremetjew, S.-Y. Yong, R. Lopez, S. Hunter, InterProScan 5: genome-scale protein function classification Bioinformatics. ,vol. 30, pp. 1236- 1240 ,(2014) , 10.1093/BIOINFORMATICS/BTU031