ajout commandes

16S_workflow.sh

@@ -37,9 +37,13 @@ sed -i 's/ //g' fasta/amplicon.fasta
 # CREATE OTU
 # DEDUPLICATION
 mkdir otu
-soft/vsearch --derep_fulllength fasta/amplicon.fasta --output otu/fulllength_otu
-soft/vsearch --derep_prefix fasta/amplicon.fasta --output otu/prefix_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
 
 # REMOVING SINGLETON
-soft/vsearch --derep_fulllength fasta/amplicon.fasta --output otu/fulllength_min10_otu --minuniquesize 10
-soft/vsearch --derep_prefix fasta/amplicon.fasta --output otu/prefix_min10_otu --minuniquesize 10
+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
+
+# 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