Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2’s q2-feature-classifier plugin

Autor: Nicholas A. Bokulich, Benjamin D. Kaehler, Jai Ram Rideout, Matthew Dillon, Evan Bolyen, Rob Knight, Gavin A. Huttley, J. Gregory Caporaso

Publikováno v: Microbiome, Vol 6, Iss 1, Pp 1-17 (2018)

Abstract Background Taxonomic classification of marker-gene sequences is an important step in microbiome analysis. Results We present q2-feature-classifier (https://github.com/qiime2/q2-feature-classifier), a QIIME 2 plugin containing several novel m

Externí odkaz: https://doaj.org/article/551b94192d324bc7b48c97a0fc6d7a3f

mockrobiota: a Public Resource for Microbiome Bioinformatics Benchmarking

Autor: Nicholas A. Bokulich, Jai Ram Rideout, William G. Mercurio, Arron Shiffer, Benjamin Wolfe, Corinne F. Maurice, Rachel J. Dutton, Peter J. Turnbaugh, Rob Knight, J. Gregory Caporaso

Publikováno v: mSystems, Vol 1, Iss 5 (2016)

ABSTRACT Mock communities are an important tool for validating, optimizing, and comparing bioinformatics methods for microbial community analysis. We present mockrobiota, a public resource for sharing, validating, and documenting mock community data

Externí odkaz: https://doaj.org/article/aa182d80d78440c2a9049d7390b83256

Subsampled open-reference clustering creates consistent, comprehensive OTU definitions and scales to billions of sequences

Autor: Jai Ram Rideout, Yan He, Jose A. Navas-Molina, William A. Walters, Luke K. Ursell, Sean M. Gibbons, John Chase, Daniel McDonald, Antonio Gonzalez, Adam Robbins-Pianka, Jose C. Clemente, Jack A. Gilbert, Susan M. Huse, Hong-Wei Zhou, Rob Knight, J. Gregory Caporaso

Publikováno v: PeerJ, Vol 2, p e545 (2014)

We present a performance-optimized algorithm, subsampled open-reference OTU picking, for assigning marker gene (e.g., 16S rRNA) sequences generated on next-generation sequencing platforms to operational taxonomic units (OTUs) for microbial community

Externí odkaz: https://doaj.org/article/043dcb23f6bc48569887bfb4c47a95f4

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

Autor: Fernando Vargas, Matthew R. Dillon, Stephanie B. Orchanian, Mary L. Preuss, Daniel McDonald, Christian C. Abnet, J. Gregory Caporaso, Alexey V. Melnik, Claire Duvallet, Massoud Maher, Max von Hippel, Colin J. Brislawn, Jamie Morton, Kyle C. Weber, Patrick Rosenthal, Qiyun Zhu, Lauren J. McIver, Talima Pearson, Clarisse Marotz, Madeleine Ernst, Ruth E. Ley, Jiarong Guo, Tomasz Kosciolek, Jorden Kreps, Benjamin D. Kaehler, Deanna L. Gibson, Yilong Zhang, Kestrel Gorlick, Catherine A. Lozupone, Nicholas A. Bokulich, Jessica L. Metcalf, Daniel M. Durall, Paul Keim, Daniel Petras, Elmar Pruesse, Dan Knights, Emily K. Cope, Gavin M. Douglas, Sean M. Gibbons, Hannes Holste, Austin D. Swafford, Yong-Xin Liu, Sabah Ul-Hasan, Joslynn S. Lee, Benjamin J. Callahan, Mehrbod Estaki, Zhenjiang Zech Xu, Jordan E. Bisanz, Jennifer Fouquier, Lingjing Jiang, Justin J. J. van der Hooft, Ahmad Turan Naimey, Michael S. Robeson, Harriet Alexander, Jesse R. Zaneveld, Andrés Mauricio Caraballo-Rodríguez, Gavin A. Huttley, Antonio Gonzalez, Curtis Huttenhower, Anupriya Tripathi, Pauline Trinh, Mingxun Wang, Emily Vogtmann, Susan Holmes, Yunhu Wan, Rashmi Sinha, Irina Koester, William A. Walters, Yang Bai, Kyo Bin Kang, Luke R. Thompson, Christian F. Edwardson, Ricardo Silva, Pedro J. Torres, Gabriel A. Al-Ghalith, Stefan Janssen, Kyle Bittinger, Manimozhiyan Arumugam, Jonathan Warren, Alan K. Jarmusch, Lasse Buur Rasmussen, Rob Knight, Se Jin Song, Michael Shaffer, Sydney C. Morgan, Bryan D Martin, Peter J. Turnbaugh, C. Titus Brown, Jose A. Navas-Molina, Morgan G. I. Langille, Christopher R. Keefe, Benjamin Hillmann, Eric J. Alm, Evan Bolyen, Arron Shiffer, Louis-Félix Nothias, Christian Diener, Nicola Segata, Francesco Asnicar, Charles H. D. Williamson, Samuel L. Peoples, Amy D. Willis, Pieter C. Dorrestein, Adam R. Rivers, John Chase, Scott T. Kelley, Julia M. Gauglitz, Yoshiki Vázquez-Baeza, John R. Spear, Jai Ram Rideout, Asker Daniel Brejnrod, Erikka Loftfield

Publikováno v: Nature Biotechnology 37 (2019) 8
Nature Biotechnology
Nature Biotechnology, 37(8), 852-857
PMC

QIIME 2 development was primarily funded by NSF Awards 1565100 to J.G.C. and 1565057 to R.K. Partial support was also provided by the following: grants NIH U54CA143925 (J.G.C. and T.P.) and U54MD012388 (J.G.C. and T.P.); grants from the Alfred P. Slo

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::f54f79979681348f38899868524602c4
https://research.wur.nl/en/publications/reproducible-interactive-scalable-and-extensible-microbiome-data-

SunPy: A Python package for Solar Physics

Autor: Matt Earnshaw, Manas Mangaonkar, Arthur Eigenbrot, Abhigyan Bose, Ankit Agrawal, Juan Camilo Buitrago-Casas, Thomas P. Robitaille, Brigitta Sipőcz, Rishabh Sharma, Yash Kothari, Jordan Ballew, Shresth Verma, Jack Ireland, Alex Hamilton, Ole Streicher, Sarthak Jain, Tiago M. D. Pereira, Yudhik Agrawal, John G Evans, David Pérez-Suárez, S. Dacie, Michael Charlton, Agneet Chatterjee, Russell J. Hewett, Samuel Bennett, Ambar Mehrotra, Steven Christe, Ishtyaq Habib, Daniel D'Avella, Florian Mayer, Sanjeev Dubey, Igor Babuschkin, Chloé Guennou, Carlos Molina, Punyaslok Pattnaik, Freek Verstringe, Jose Ivan Campos Rozo, Kaustubh Hiware, Deepankar Sharma, Shane A. Maloney, Tomas Meszaros, Tessa D. Wilkinson, Tannmay Yadav, N. Freij, Swapnil Sharma, W. T. Barnes, Mateo Inchaurrandieta, Sophie A. Murray, Emmanuel Arias, Andrew J. Leonard, Stuart Mumford, Harsh Mathur, Rajasekhar Reddy Mekala, Nicky Chorley, James Mason, Rishabh Mishra, Dhruv Goel, Juanjo Bazán, Goran Cetusic, Nicholas A. Murphy, Michael Malocha, Arseniy Kustov, Sanskar Modi, Shashank Srikanth, S. Zahniy, Vishnunarayan K, Himanshu, Jacob, Duygu Keşkek, Norbert G. Gyenge, Andrew Hill, Pritish Chakraborty, Daniel Williams, Jaylen Wimbish, Ankit Baruah, André Chicrala, Ankit Kumar, Michael Mueller, Airmansmith, Garrison Taylor, Rajul Srivastava, David Stansby, Adrian M. Price-Whelan, Asish Panda, Mickaël Schoentgen, Ruben De Visscher, Yasintoda, Yash Krishan, Quinn Arbolante, Matt Bates, Sourav Ghosh, Reid Gomillion, Nitin Choudhary, Simon Liedtke, Monica G. Bobra, Daniel Ryan, Bernhard M. Wiedemann, Fionnlagh Mackenzie Dover, Abigail L. Stevens, Erik M. Bray, Albert Y. Shih, Brandon Stone, Dominik Stańczak, Naman, Jongyeob Park, Gulshan Kumar, Joseph Letts, Priyank Lodha, Dumindu Buddhika, Sudarshan Konge, Ankit, Larry Manley, Trung Kien Dang, V. Keith Hughitt, Akramul Haque, Michael S. Kirk, Jamescalixto, Matthew Mendero, Benjamin Mampaey, Laura A. Hayes, Yash Jain, Andrew Inglis, Prateek Chanda, Yash Sharma, Kalpesh Krishna, Jai Ram Rideout

Publikováno v: Journal of Open Source Software. 5:1832

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::410570729b4c07326fd3ce821a1a89f7
https://doi.org/10.21105/joss.01832