swarm step

II - Processing steps/obiclean_processing.sh

-obiclean -r 0.05 -H Aquarium_2.fasta > PipelineA_Aquarium_2.fasta
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+obiclean -r 0.05 -H Aquarium_2.fasta > PipelineA_Aquarium_2.fasta
+
+## here, the command only returns only the sequences tagged "head" by 
+## the algorithm, and the chosen ratio is 0.05
\ No newline at end of file

II - Processing steps/swarm_processing.sh

+## use the swarm command to make the gathering :
+swarm -z -d 1 -o stats_Aquarium_2.txt -w Aquarium_2.clustered.fasta < Aquarium_2.fasta
+
+## "-z" option permits to accept the abundance in the header, provided
+## that there is no space in the header and that the value is preceded
+## by "size="
+
+## "-d" is the maximal number of differences tolerated between two
+## sequences to be gathered in the same OTU (1 here)
+
+## "-o" option returns a ".txt" file in which each line corresponds to
+## an OTU with all the amplicons belonging to this OTU
+
+## "-w" option gives a "fasta" file with the representative sequence of 
+## each OTU