Computational protocol: Forensic analysis of the microbiome of phones and shoes

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Protocol publication

[…] Unpaired reads of length 151 bp for both the time series and biogeographic studies were clustered together at 97% identity using the Quantitative Insights Into Microbial Ecology (QIIME) script pick_open_reference_otus.py, with the May 2013 release of Greengenes (greengenes.lbl.gov) as the reference. OTUs comprising only a single read were discarded, and samples were rarified to an even depth of 1,000 reads.Analysis of beta-diversity was performed by calculating the pairwise weighted and unweighted UniFrac [] distance between each pair of samples, and the resulting distance matrix was used for all downstream statistical tests of sample similarity. The significance of sample groupings was assessed using PERMANOVA (QIIME’s compare_categories.py script) and statistical significance was calculated by comparing the Pseudo-F statistic to a distribution generated by 10,000 permutations of the randomized dataset. […]

Pipeline specifications

Software tools QIIME, UniFrac
Application 16S rRNA-seq analysis
Organisms Homo sapiens