1) get OTU cluster of similar sequences (97% itentity)

2) select one representative sequences for each OTU

3) annotate OTU cluster with known taxonomy (consider OTU representative sequences without database hits as "unkown")

4) create table (biom format) containing OTU abundance of all samples, and taxonomy information for further analysis

→ QIIME tutorial: OTU picking
→ 18S Fungi OTU picking

→ SILVA OTU annotation

pick_open_reference_otus.py -i $PWD/SEQ/seqs.fna -o $PWD/OTU/ -p $PWD/otu_settings.txt

Results:
  otu_table_mc2_w_tax.biom   OTU abundance table of all samples, including taxonomy  
  rep_set.fna   representative sequences for each OTU cluster
  rep_set.tre   phylogenetic tree based on representative OTU sequenes

Get OTU cluster using usearch

same as above, but using another sequence clustering algorithm

# install sequence cluster algorithm: → usearch

# set location of reference sequence file "97_otus.fasta"

REFSEQS=/path/to/my/qiime1/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/rep_set/97_otus.fasta

# allow taxonomic annotation of sequences in reverse orientation
echo 'pick_otus:enable_rev_strand_match True' > otu_settings.txt 

# run otu picking with usearch61

pick_open_reference_otus.py -i $PWD/SEQ/seqs.fna -o $PWD/OTU/ -r $REFSEQS -s 0.1 -m usearch61 -p $PWD/otu_settings.txt

Get OTU & read count per sample

biom summarize-table -i OTU/otu_table_mc2_w_tax_no_pynast_failures.biom --qualitative -o stats_OTUs_per_sample.txt

# Get number of reads per sample (not normalized OTU table)
biom summarize-table -i OTU/otu_table_mc2_w_tax_no_pynast_failures.biom -o stats_reads_per_sample.txt

Visualize OTU table as heatmap

make_otu_heatmap.py -i otu_table_mc2_w_tax_no_pynast_failures.biom -o otu_heatmap.pdf

Convert OTU table into text file

# Convert OTU .biom file to .tsv text file
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

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read more
http://qiime.org/tutorials/otu_picking.html
http://qiime.org/scripts/pick_open_reference_otus.html
http://biom-format.org/documentation/summarizing_biom_tables.html