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SILVA

QIIME - OTU annotation using SILVA reference database

How to get SILVA annotated OTU's

SILVA is free for academic/non-commercial users. For commercial use, see SILVA license

Download SILVA reference database & decompress

wget https://www.arb-silva.de/fileadmin/silva_databases/qiime/Silva_128_release.tgz
wget https://www.arb-silva.de/fileadmin/silva_databases/qiime/Silva_128_notes.txt
tar -zxvf Silva_128_release.tgz
https://www.arb-silva.de/download/archive/qiime/

# move folder  "SILVA_128_QIIME_release/"  to a permanent database directory, accessible for example:
/home/myname/data/SILVA_128_QIIME_release/

Create OTU setting file

# create new parameter file for pick_open_reference_otus.py and add setting lines (adapt correct database path)
 > otu_SILVA_settings.txt
echo "pick_otus:enable_rev_strand_match True" >> otu_SILVA_settings.txt
echo "align_seqs.py:template_fp /home/myname/data/SILVA_128_QIIME_release/core_alignment/core_alignment_SILVA128.fna" >> otu_SILVA_settings.txt
echo "filter_alignment:allowed_gap_frac 0.80" >> otu_SILVA_settings.txt
echo "filter_alignment:entropy_threshold 0.10" >> otu_SILVA_settings.txt
echo "filter_alignment:suppress_lane_mask_filter True" >> otu_SILVA_settings.txt
echo "assign_taxonomy:reference_seqs_fp /home/myname/data/SILVA_128_QIIME_release/rep_set/rep_set_all/97/97_otus.fasta" >> otu_SILVA_settings.txt
echo "assign_taxonomy:id_to_taxonomy_fp /home/myname/data/SILVA_128_QIIME_release/taxonomy/taxonomy_all/97/taxonomy_7_levels.txt" >> otu_SILVA_settings.txt


# check content of parameter file
cat otu_SILVA_settings.txt
pick_otus:enable_rev_strand_match True
align_seqs.py:template_fp /home/myname/data/SILVA_128_QIIME_release/core_alignment/core_alignment_SILVA128.fna
filter_alignment:allowed_gap_frac 0.80
filter_alignment:entropy_threshold 0.10
filter_alignment:suppress_lane_mask_filter True
assign_taxonomy:reference_seqs_fp /home/myname/data/SILVA_128_QIIME_release/rep_set/rep_set_all/97/97_otus.fasta
assign_taxonomy:id_to_taxonomy_fp /home/myname/data/SILVA_128_QIIME_release/taxonomy/taxonomy_all/97/taxonomy_7_levels.txt


Run OTU clustering and SILVA annotation

# run OTU picking
pick_open_reference_otus.py -i seqs.fna -p otu_SILVA_settings.txt -r /home/myname/data/SILVA_128_QIIME_release/rep_set/rep_set_all/97/97_otus.fasta -o OTU_SILVA


# Result
OTU_SILVA/otu_table_mc2_w_tax_no_pynast_failures.biom   # OTU abundance table of all samples, including taxonomy (SILVA annotation) 


# convert OTU abundance table into a tab separated text file, readable with Excel
biom convert -i otu_table_mc2_w_tax_no_pynast_failures.biom -o otu_table_mc2_w_tax_no_pynast_failures.tsv --to-tsv --header-key taxonomy




https://www.arb-silva.de/download/archive/qiime/
https://groups.google.com/forum/#!msg/qiime-forum/