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16S_workflow
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ajout etape clustering

nicolas-zimmermann 5 years ago
parent
21880df223
commit
8165ca41a8
1 changed files with 11 additions and 6 deletions
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  1. 11 6
      16S_workflow.sh

+ 11 - 6
16S_workflow.sh View File

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