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Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities
Abstract
mothur aims to be a comprehensive software package that allows users to use a single piece of software to analyze community sequence data. It builds upon previous tools to provide a flexible and powerful software package for analyzing sequencing data. As a case study, we used mothur to trim, screen, and align sequences; calculate distances; assign sequences to operational taxonomic units; and describe the α and β diversity of eight marine samples previously characterized by pyrosequencing of 16S rRNA gene fragments. This analysis of more than 222,000 sequences was completed in less than 2 h with a laptop computer.
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“MOTHUR clustering scores indels as a single gap penalty, and we found it worked to effectively cluster LTR elements into accurate family groups.”
From RepeatModeler2 for automated genomic discovery of transposable element families (2020) · cites this paper as Schloss et al. 2009
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Lozupone, C., & Knight, R. (2005) · Applied and Environmental Microbiology · doi:10.1128/aem.71.12.8228-8235.2005 · Cited by 8,227
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DADA2: High–resolution sample inference from Illumina amplicon data
Callahan, B. J., McMurdie, P. J., Rosen, M. J., Han, A. W., Johnson, A. J. A., & Holmes, S. P. (2016) · Nature Methods · doi:10.1038/nmeth.3869 · Cited by 35,698
QIIME allows analysis of high-throughput community sequencing data
Caporaso, J. G., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F. D., Costello, E. K., Fierer, N., Peña, A. G., Goodrich, J. K., Gordon, J. I., et al. (2010) · Nature Methods · doi:10.1038/nmeth.f.303 · Cited by 34,887
The SILVA ribosomal RNA gene database project: improved data processing and web-based tools
Quast, C., Pruesse, E., Yilmaz, P., Gerken, J., Schweer, T., Yarza, P., Peplies, J., & Glöckner, F. O. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks1219 · Cited by 33,055
Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2
Bolyen, E., Rideout, J. R., Dillon, M. R., Bokulich, N. A., Abnet, C. C., Al-Ghalith, G. A., Alexander, H., Alm, E. J., Arumugam, M., Asnicar, F., et al. (2019) · Nature Biotechnology · doi:10.1038/s41587-019-0209-9 · Cited by 23,742
Metagenomic biomarker discovery and explanation
Segata, N., Izard, J., Waldron, L., Gevers, D., Miropolsky, L., Garrett, W. S., & Huttenhower, C. (2011) · Genome Biology · doi:10.1186/gb-2011-12-6-r60 · Cited by 16,192
Metadata
- Authors
- Schloss, P. D., Westcott, S. L., Ryabin, T., Hall, J. R., Hartmann, M., Hollister, E. B., Lesniewski, R. A., Oakley, B. B., Parks, D. H., Robinson, C. J., Sahl, J. W., Stres, B., Thallinger, G. G., Van Horn, D. J., & Weber, C. F.
- Affiliations
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts
- Department of Biology, University of New Mexico, Albuquerque, New Mexico
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
- Department of Soil and Crop Sciences, Texas A&M University, College Station, Texas
- Department of Soil, Water, and Climate, University of Minnesota, St. Paul, Minnesota
- Department of Biological Sciences, University of Warwick, Coventry, United Kingdom
- Faculty of Computer Science, Dalhousie University, Halifax, NS, Canada
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan
- Environmental Science and Engineering, Colorado School of Mines, Golden, Colorado
- Department of Animal Science, University of Ljubljana, Ljubljana, Slovenia
- Institute for Genomics and Bioinformatics, Graz University of Technology, Graz, Austria
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Lousiana
- Venue
- Applied and Environmental Microbiology
- Publisher
- American Society for Microbiology
- Published
- 2009-12
- Volume
- 75
- Issue
- 23
- Pages
- 7537-7541
- ISSN
- 0099-2240
- 1098-5336
- Cited by
- 19,549
- References
- 1
- Language
- en
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