Online tools Population Dynamics

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The pipeline will use Dada2 package to product an amplicon sequence variant (ASV) table ( an analogue of the traditional OTU table), which records for each sample the number of times each exact amplicon sequence variant was observed.
For 16S/18S amplicon sequencing, taxonomy is assigned to these sequence variants by comparison to a training set of reference sequences with known taxonomy (from RDP, Greengenes or SILVA databases).
The alpha-diversity plot and the top20 distribution of family levels are then ploted with phyloseq package

Author(s)

M. Massaviol, K. Belkhir and E. Desmarais


Version

1


Subsections

Pipeline