Feature requests / bug reports should be submitted via the official GitHub repository.
Citations
If you find mOTUs useful in your work, please cite: Cultivation-independent genomes greatly expand taxonomic-profiling capabilities of mOTUs across various environments Hans-Joachim Ruscheweyh*, Alessio Milanese*, Lucas Paoli, Nicolai Karcher, Quentin Clayssen, Marisa Isabell Keller, Jakob Wirbel, Peer Bork, Daniel R Mende, Georg Zeller#, Shinichi Sunagawa#. Microbiome 10, Article number: 212 (2022): https://doi.org/10.1186/s40168-022-01410-z
For mOTUs2: Microbial abundance, activity and population genomic profiling with mOTUs2 Alessio Milanese*, Daniel R Mende*, Lucas Paoli, Guillem Salazar, Hans-Joachim Ruscheweyh, Miguelangel Cuenca, Pascal Hingamp, Renato Alves, Paul I Costea, Luis P Coelho, T Sebastian B Schmidt, Alexandre Almeida, Alex L Mitchell, Robert D Finn, Jaime Huerta-Cepas, Peer Bork, Georg Zeller#, Shinichi Sunagawa#. Nature Communications 10, Article number: 1014 (2019): https://doi.org/10.1038/s41467-019-08844-4
For mOTUs1: Metagenomic species profiling using universal phylogenetic marker genes Shinichi Sunagawa, Daniel R Mende, Georg Zeller, Fernando Izquierdo-Carrasco, Simon A Berger, Jens Roat Kultima, Luis Pedro Coelho, Manimozhiyan Arumugam, Julien Tap, Henrik Bjørn Nielsen, Simon Rasmussen, Søren Brunak, Oluf Pedersen, Francisco Guarner, Willem M de Vos, Jun Wang, Junhua Li, Joël Doré, S Dusko Ehrlich, Alexandros Stamatakis, Peer Bork. Nature Methods 10, 1196–1199 (2013): https://doi.org/10.1038/nmeth.2693
Protocol
For more information on how to run mOTUs, see: mOTUs: Profiling Taxonomic Composition, Transcriptional Activity and Strain Populations of Microbial Communities Hans-Joachim Ruscheweyh*, Alessio Milanese*, Lucas Paoli, Anna Sintsova, Daniel R Mende, Georg Zeller#, Shinichi Sunagawa# Current Protocols 1, e218 (2021): https://doi.org/10.1002/cpz1.218
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mOTUs v1
The codebase of the first version of mOTUs can be found here.
License
mOTUs is published under the GPL-3.0 license.