The DOI matches its Crossref record; 48 of the 48 references it cites were found in a registry or an index.
FROGS: Find, Rapidly, OTUs with Galaxy Solution
Open accessAbstract
Motivation: Metagenomics leads to major advances in microbial ecology and biologists need user friendly tools to analyze their data on their own. Results: This Galaxy-supported pipeline, called FROGS, is designed to analyze large sets of amplicon sequences and produce abundance tables of Operational Taxonomic Units (OTUs) and their taxonomic affiliation. The clustering uses Swarm. The chimera removal uses VSEARCH, combined with original cross-sample validation. The taxonomic affiliation returns an innovative multi-affiliation output to highlight databases conflicts and uncertainties. Statistical results and numerous graphical illustrations are produced along the way to monitor the pipeline. FROGS was tested for the detection and quantification of OTUs on real and in silico datasets and proved to be rapid, robust and highly sensitive. It compares favorably with the widespread mothur, UPARSE and QIIME. Availability and implementation: Source code and instructions for installation: https://github.com/geraldinepascal/FROGS.git. A companion website: http://frogs.toulouse.inra.fr. Supplementary information: Supplementary data are available at Bioinformatics online.
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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
Cutadapt removes adapter sequences from high-throughput sequencing reads
Martin, M. (2011) · EMBnet.journal · doi:10.14806/ej.17.1.200 · Cited by 33,889
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
BLAST+: architecture and applications
Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J., Bealer, K., & Madden, T. L. (2009) · BMC Bioinformatics · doi:10.1186/1471-2105-10-421 · Cited by 22,074
phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data
McMurdie, P. J., & Holmes, S. (2013) · PLoS ONE · doi:10.1371/journal.pone.0061217 · Cited by 21,322
Search and clustering orders of magnitude faster than BLAST
Edgar, R. C. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq461 · Cited by 20,826
Naïve Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy
Wang, Q., Garrity, G. M., Tiedje, J. M., & Cole, J. R. (2007) · Applied and Environmental Microbiology · doi:10.1128/aem.00062-07 · Cited by 19,885
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., et al. (2009) · Applied and Environmental Microbiology · doi:10.1128/aem.01541-09 · Cited by 19,549
UPARSE: highly accurate OTU sequences from microbial amplicon reads
Edgar, R. C. (2013) · Nature Methods · doi:10.1038/nmeth.2604 · Cited by 16,707
FLASH: fast length adjustment of short reads to improve genome assemblies
Magoč, T., & Salzberg, S. L. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr507 · Cited by 15,366
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de Lorgeril, J., Lucasson, A., Petton, B., Toulza, E., Montagnani, C., Clerissi, C., Vidal-Dupiol, J., Chaparro, C., Galinier, R., Escoubas, J.-M., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-06659-3 · Cited by 308
Pauvert, C., Buée, M., Laval, V., Edel-Hermann, V., Fauchery, L., Gautier, A., Lesur, I., Vallance, J., & Vacher, C. (2019) · Fungal Ecology · doi:10.1016/j.funeco.2019.03.005 · Cited by 253
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Self-citationShift in skin microbiota of Western European women across aging
Jugé, R., Rouaud-Tinguely, P., Breugnot, J., Servaes, K., Grimaldi, C., Roth, M.-P., Coppin, H., & Closs, B. (2018) · Journal of Applied Microbiology · doi:10.1111/jam.13929 · Cited by 112
Metadata
- Authors
- Escudié, F., Auer, L., Bernard, M., Mariadassou, M., Cauquil, L., Vidal, K., Maman, S., Hernandez-Raquet, G., Combes, S., & Pascal, G.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2017-12-07
- Volume
- 34
- Issue
- 8
- Pages
- 1287-1294
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2774551105
- Cited by
- 1,018
- References
- 48
- FWCI
- 23.88
- Type
- journal article
- Language
- en
- Open access
- bronze
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- Escudié, F., Auer, L., Bernard, M., Mariadassou, M., Cauquil, L., Vidal, K., Maman, S., Hernandez-Raquet, G., Combes, S., & Pascal, G. (2018). FROGS: Find, Rapidly, OTUs with Galaxy Solution. Bioinformatics. https://doi.org/10.1093/bioinformatics/btx791
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