nzimmermann
/
16S_workflow
1
0
Fork 0
Code Issues Pull Requests Releases Wiki Activity

ajout etape clustering

master
nicolas-zimmermann 2019-10-24 11:38:01 +02:00
parent 21880df223
commit 8165ca41a8
1 changed files with 11 additions and 6 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

17
16S_workflow.sh
View File

@ -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