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Processing 16S rRNA sequencing

PD Peter J Diebold
FN Felicia N New
MH Michael Hovan
MS Michael J Satlin
IB Ilana L Brito
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Raw reads were merged using usearch (Edgar, 2010) (V 11.0.667) -fastq_mergepairs (maxdiffs: 20, pctid: 85, minmergelen: 283, maxmergelen: 293) before trimming primers and quality filtering with usearch -fastq_filter (maxee: 1.0). Unique reads were filtered using usearch -fastx_uniques, and OTUs were clustered based on 97% identity with usearch -cluster_otus. OTU tables were generated with usearch -otutab, and taxonomy was assigned with RDP classifier implemented in MOTHUR classify.sequs (1.38.1) against silva v132. Rarefaction curves were generated using QIIME1 (Caporaso et al., 2010) (v1.9) multiple_rarefaction.py (-m 10, -x 100000, -s 100, -n 5, -k). Scripts have been uploaded to the GitHub repository (https://github.com/pjdiebold/OIL-PCR_Linking_plasmid-based_beta-lactamases; Diebold, 2021; copy archived at swh:1:rev:6d5b25dfa6d67703f06f74c24f7efe27bcf9d8dd).

Copyright and License information:  ©2021, Diebold et al
This article is distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use and redistribution provided that the original author and source are credited.

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