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16S_workflow
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added annotation part

master
nicolas-zimmermann 2019-10-24 12:15:12 +02:00
parent 8ff28a2a57
commit 721e404673
1 changed files with 5 additions and 2 deletions
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16S_workflow.sh
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@ -48,7 +48,10 @@ soft/vsearch --uchime_denovo fasta/prefix.fasta --nonchimeras fasta/prefix_nochi
# CLUSTERING # CLUSTERING
otu=">OTU_" otu=">OTU_"
vsearch --cluster_fast fasta/prefix_nochim.fasta --id 0.97 --centroids otu/centroids.fasta --relabel $otu vsearch --cluster_fast fasta/prefix_nochim.fasta --id 0.97 --centroids otu/otu.fasta --relabel $otu
# ABONDANCE # ABONDANCE
vsearch --usearch_global fasta/amplicon.fasta --db otu/clusters.fasta --id 0.97 --otutabout otu/abondance_table.txt vsearch --usearch_global fasta/amplicon.fasta --db otu/otu.fasta --id 0.97 --otutabout otu/abondance_table.txt
# ANNOTATION
soft/vsearch --usearch_global otu/otu.fasta --db databases/mock_16S_18S.fasta --id 0.97 --top_hits_only --userfields query+target --userout otu/annotation.txt