Commit 0cbd3379 authored by Bastien Macé's avatar Bastien Macé
Browse files

swarm step

parent 0386a574
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
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## 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
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