PICRUSt2: An improved and customizable approach for metagenome inference
作者： Gavin M. Douglas , Vincent J. Maffei , Jesse Zaneveld , Svetlana N. Yurgel , James R. Brown
DOI: 10.1101/672295
关键词: Microbial population biology 、 Computational biology 、 Gene family 、 Marker gene 、 Computer science 、 Genome 、 Inference 、 Metagenomics
摘要: 抄録< jats: p> One major limitation of microbial community marker gene sequencing is that it does not provide direct information on the functional composition of sampled communities. Here, we present PICRUSt2 (< jats: ext-link xmlns: xlink=" http://www. w3. org/1999/xlink" ext-link-type=" uri" xlink: href=" https://github. com/picrust/picrust2"> https://github. com/picrust/picrust2), which expands the capabilities of the original PICRUSt method< jats: sup> 1 to predict the functional potential of a community based on …
sci-hub.st 参考文章(32)
Lauren E. Gillies, J. Cameron Thrash, Sergio deRada, Nancy N. Rabalais, Olivia U. Mason, Archaeal enrichment in the hypoxic zone in the northern Gulf of Mexico. Environmental Microbiology. ,vol. 17, pp. 3847- 3856 ,(2015) , 10.1111/1462-2920.12853
Se-Ran Jun, Michael S. Robeson, Loren J. Hauser, Christopher W. Schadt, Andrey A. Gorin, PanFP: pangenome-based functional profiles for microbial communities BMC Research Notes. ,vol. 8, pp. 479- 479 ,(2015) , 10.1186/S13104-015-1462-8
I-Min A. Chen, Victor M. Markowitz, Ken Chu, Iain Anderson, Konstantinos Mavromatis, Nikos C. Kyrpides, Natalia N. Ivanova, Improving Microbial Genome Annotations in an Integrated Database Context PLoS ONE. ,vol. 8, pp. e54859- ,(2013) , 10.1371/JOURNAL.PONE.0054859
T. Z. DeSantis, P. Hugenholtz, N. Larsen, M. Rojas, E. L. Brodie, K. Keller, T. Huber, D. Dalevi, P. Hu, G. L. Andersen, Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB Applied and Environmental Microbiology. ,vol. 72, pp. 5069- 5072 ,(2006) , 10.1128/AEM.03006-05
M. Kanehisa, S. Goto, Y. Sato, M. Furumichi, M. Tanabe, KEGG for integration and interpretation of large-scale molecular data sets Nucleic Acids Research. ,vol. 40, pp. 109- 114 ,(2012) , 10.1093/NAR/GKR988
V. M. Markowitz, I.-M. A. Chen, K. Palaniappan, K. Chu, E. Szeto, Y. Grechkin, A. Ratner, B. Jacob, J. Huang, P. Williams, M. Huntemann, I. Anderson, K. Mavromatis, N. N. Ivanova, N. C. Kyrpides, IMG: the integrated microbial genomes database and comparative analysis system Nucleic Acids Research. ,vol. 40, pp. 115- 122 ,(2012) , 10.1093/NAR/GKR1044
Kathrin P. Aßhauer, Bernd Wemheuer, Rolf Daniel, Peter Meinicke, Tax4Fun: predicting functional profiles from metagenomic 16S rRNA data. Bioinformatics. ,vol. 31, pp. 2882- 2884 ,(2015) , 10.1093/BIOINFORMATICS/BTV287
Morgan G I Langille, Jesse Zaneveld, J Gregory Caporaso, Daniel McDonald, Dan Knights, Joshua A Reyes, Jose C Clemente, Deron E Burkepile, Rebecca L Vega Thurber, Rob Knight, Robert G Beiko, Curtis Huttenhower, Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences Nature Biotechnology. ,vol. 31, pp. 814- 821 ,(2013) , 10.1038/NBT.2676
Daniel H Haft, Jeremy D Selengut, Owen White, The TIGRFAMs database of protein families Nucleic Acids Research. ,vol. 31, pp. 371- 373 ,(2003) , 10.1093/NAR/GKG128
Huttenhower Curtis, Martin J Blaser, Gevers Dirk, Karthik C Kota, Knight Rob, Bo Liu, Lu Wang, Abubucker Sahar, James R White, Jonathan H Badger, Asif T Chinwalla, Heather H Creasy, Ashlee M Earl, Michael G Fitzgerald, Robert S Fulton, Michelle G Giglio, Mitreva Makedonka, Erica J Sodergren, Elizabeth A Lobos, Donna M Muzny, Magrini Vincent, Versalovic James, Madupu Ramana, John C Martin, Aye M Wollam, Kim C Worley, Jennifer R Wortman, Sarah K Young, Zeng Qiandong, Kjersti M Aagaard, Olukemi O Abolude, Eric J Alm, Alvarado Lucia, Gary L Andersen, Anderson Scott, Appelbaum Elizabeth, Harindra M Arachchi, Armitage Gary, Cesar A Arze, Ayvaz Tulin, Carl C Baker, Begg Lisa, Belachew Tsegahiwot, Bhonagiri Veena, Bihan Monika, Bloom Toby, Bonazzi Vivien, J Paul Brooks, Gregory A Buck, Christian J Buhay, Dana A Busam, Joseph L Campbell, Shane R Canon, Brandi L Cantarel, SG Patrick, I Min A Chen, Chen Lei, Chhibba Shaila, Chu Ken, Dawn M Ciulla, Jose C Clemente, Sandra W Clifton, Conlan Sean, Crabtree Jonathan, Mary A Cutting, Noam J Davidovics, Catherine C Davis, Todd Z Desantis, Deal Carolyn, Kimberley D Delehaunty, Floyd E Dewhirst, Deych Elena, Ding Yan, David J Dooling, Shannon P Dugan, A Scott Durkin, Robert C Edgar, Rachel L Erlich, Candace N Farmer, Ruth M Farrell, Faust Karoline, Feldgarden Michael, Victor M Felix, Fisher Sheila, Anthony A Fodor, Larry J Forney, Foster Leslie, Friedman Jonathan, Dennis C Friedrich, Catrina C Fronick, Lucinda L Fulton, Gao Hongyu, Garcia Nathalia, Giannoukos Georgia, Giblin Christina, Maria Y Giovanni, Jonathan M Goldberg, Goll Johannes, Gonzalez Antonio, Griggs Allison, Gujja Sharvari, Brian J Haas, Holli A Hamilton, Emily L Harris, Theresa A Hepburn, Herter Brandi, Diane E Hoffmann, Michael E Holder, Howarth Clinton, Katherine H Huang, Susan M Huse, Izard Jacques, Janet K Jansson, Jiang Huaiyang, Jordan Catherine, Joshi Vandita, James A Katancik, Wendy A Keitel, Scott T Kelley, Kells Cristyn, Nicholas B King, Knights Dan, Heidi H Kong, Koren Omry, Koren Sergey, Christie L Kovar, Nikos C Kyrpides, Patricio S La Rosa, Sandra L Lee, Katherine P Lemon, Lennon Niall, Cecil M Lewis, Lewis Lora, Ruth E Ley, Li Kelvin, Liolios Konstantinos, Liu Yue, Catherine A Lozupone, R Dwayne Lunsford, Madden Tessa, Anup A Mahurkar, Peter J Mannon, Elaine R Mardis, Victor M Markowitz, Mavromatis Konstantinos, Jamison M Mccorrison, Mcdonald Daniel, Mcewen Jean, Amy L Mcguire, Mcinnes Pamela, Structure, function and diversity of the healthy human microbiome Nature. ,vol. 486, pp. 207- 214 ,(2012) , 10.1038/NATURE11234