Computational protocol: Normalization of the microbiota in patients after treatment for colonic lesions

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Protocol publication

[…] The mothur software package (v1.37.5) was used to process the 16S rRNA gene sequences and has been previously described []. The general workflow using mothur included merging paired-end reads into contigs, filtering for low quality contigs, aligning to the SILVA database [], screening for chimeras using UCHIME [], classifying with a naive Bayesian classifier using the Ribosomal Database Project (RDP) [], and clustered into operational taxonomic units (OTUs) using a 97% similarity cutoff with an average neighbor clustering algorithm []. The number of sequences for each sample was rarefied to 10523 to minimize the impacts of uneven sampling. […]

Pipeline specifications

Software tools mothur, UCHIME
Application 16S rRNA-seq analysis
Organisms Homo sapiens, Bacteria
Diseases Adenoma, Carcinoma, Colonic Diseases, Colorectal Neoplasms