From 8165ca41a8de0caca057616b90026b495e1daaad Mon Sep 17 00:00:00 2001 From: nicolas-zimmermann Date: Thu, 24 Oct 2019 11:38:01 +0200 Subject: [PATCH] ajout etape clustering --- 16S_workflow.sh | 17 +++++++++++------ 1 file changed, 11 insertions(+), 6 deletions(-) diff --git a/16S_workflow.sh b/16S_workflow.sh index 6ea9f35..406752a 100755 --- a/16S_workflow.sh +++ b/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 +