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/