deletions | additions       diff --git a/Sequence_Quality_Control_and_Analysis.tex b/Sequence_Quality_Control_and_Analysis.tex  index 473f1e8..d0e66e0 100644  --- a/Sequence_Quality_Control_and_Analysis.tex  +++ b/Sequence_Quality_Control_and_Analysis.tex 
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sequences and corresponding taxonomic annotations, \citep{22134646}) for 16S  reads or the Silva LSU database (Ref set, version 115, EMBL taxonomic  annotations, \citep{23193283}) for the 23S reads as reference. We used the  default parameters for the algorithm (i.e. minimum consensus of 51\% at any rank, minimum sequence identity for hits at 90\% and the maximum accepted hits  value was set to 3). 
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coordinate ordinations were performed using the Bray-Curtis similarity measure  for pairwise library comparisons. Adonis tests employed the default value for  number of permutations (999) ("adonis" function in Vegan R package,  \citet{vegan}). Principal coordinates of OTUs were found by averaging site principal coordinate values for each OTU with OTU relative abundance values  (within sites) as weights. The principal coordinate OTU weighted averages were  then expanded to match the site-wise variances \citep{vegan}.