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16S_workflow
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16S_workflow.sh
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@ -37,18 +37,13 @@ sed -i 's/ //g' fasta/amplicon.fasta
# CREATE OTU
# DEDUPLICATION
mkdir otu
soft/vsearch --derep_fulllength fasta/amplicon.fasta --output fasta/fulllength.fasta
soft/vsearch --derep_prefix fasta/amplicon.fasta --output fasta/prefix.fasta
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_prefix fasta/amplicon.fasta --output fasta/prefix_min10.fasta --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 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
vsearch --usearch_global fasta/amplicon.fasta --db otu/clusters.fasta --id 0.97 --otutabout otu/abondance_table.txt
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