ajout etape clustering

16S_workflow.sh

@@ -37,13 +37,18 @@ sed -i 's/ //g' fasta/amplicon.fasta
 # CREATE OTU
 # DEDUPLICATION
 mkdir otu
-soft/vsearch --derep_fulllength fasta/amplicon.fasta --output otu/fulllength_otu.fasta
-soft/vsearch --derep_prefix fasta/amplicon.fasta --output otu/prefix_otu.fasta
+soft/vsearch --derep_fulllength fasta/amplicon.fasta --output fasta/fulllength.fasta
+soft/vsearch --derep_prefix fasta/amplicon.fasta --output fasta/prefix.fasta
 
 # REMOVING SINGLETON
-soft/vsearch --derep_fulllength fasta/amplicon.fasta --output otu/fulllength_min10_otu.fasta --minuniquesize 10
-soft/vsearch --derep_prefix fasta/amplicon.fasta --output otu/prefix_min10_otu.fasta --minuniquesize 10
+soft/vsearch --derep_prefix fasta/amplicon.fasta --output fasta/prefix_min10.fasta --minuniquesize 10
 
 # REMOVING CHIMERAS
-soft/vsearch --uchime_denovo otu/prefix_min10_otu.fasta --nonchimeras otu/prefix_min10_nochim_otu.fasta
-soft/vsearch --uchime_denovo otu/fulllength_min10_otu.fasta --nonchimeras otu/fulllength_min10_nochim_otu.fasta
+soft/vsearch --uchime_denovo fasta/prefix.fasta --nonchimeras fasta/prefix_nochim.fasta
+
+# CLUSTERING
+otu=">OTU_"
+vsearch --cluster_fast fasta/prefix_nochim.fasta --id 0.97 --centroids otu/centroids.fasta --relabel $otu
+
+# ABONDANCE
+