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Preprint

Taxonomic analysis of 16S rRNA reads extracted from metagenome

VC Víctor J. Carrión
VC Viviane Cordovez
MM Marnix H. Medema
JR Jos M. Raaijmakers

Last updated date: Jan 13, 2023 Views: 475 Forks: 0

original An abbreviated version of this protocol was published in Science in Nov, 2019
Pathogen-induced activation of disease-suppressive functions in the endophytic root microbiome
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1. a more detailed protocol can be found here:
https://github.com/nioo-knaw/orochi/blob/0.1/Snakefile#L500
2. Please find in the zenodo link the detals of the snakemake and the extraction of 16S reads from the metagenome.


https://zenodo.org/record/3405565#.YGWXxNztZhE


Also see below the description for the sup material:

4.Taxonomic analysis of 16S rRNA reads extracted from metagenome Ribosomal RNA reads were extracted from the quality and contamination filtered reads using a kmer strategy in BBDuk from the BBMap tool suite (54). These rRNA reads were aligned to SILVA 119 (55) reference set provided by Qiime (56) using the usearch_global algorithm implemented in VSEARCH (57). The alignment in usearch format (uc) was converted to a BIOM file with the biom 2.1.5 package (58) and the from-uc flag. All steps where implemented in a Snakemake workflow (59). The OTU table was filtered using QIIME (1.9.1) custom scripts (60).


I have asked Mattias de Hollander to give more details if possible. Also if you have more questions, do not hesitate in contacting me.

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How to cite：
Readers should cite both the Bio-protocol preprint and the original research article where this protocol was used:
  1. Carrión, V, Cordovez, V, Medema, M and Raaijmakers, J(2023). Taxonomic analysis of 16S rRNA reads extracted from metagenome. Bio-protocol Preprint. bio-protocol.org/prep2115.
  2. Carrión, V. J., Perez-Jaramillo, J., Cordovez, V., Tracanna, V., Hollander, M. D., Ruiz-Buck, D., Mendes, L. W., Ijcken, W. F. V., Gomez-Exposito, R., Elsayed, S. S., Mohanraju, P., Arifah, A., Oost, J. V. D., Paulson, J. N., Mendes, R., Wezel, G. P. V., Medema, M. H. and Raaijmakers, J. M.(2019). Pathogen-induced activation of disease-suppressive functions in the endophytic root microbiome. Science 366(6465). DOI: 10.1126/science.aaw9285

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