OTU biom table

→ OTU (Operational taxonomic unit)

Get OTU count from .biom table

print_biom_table_summary.py # old command

raw sequence counts

# Get number of OTU's per sample (not normalized OTU table)

biom summarize-table -i otu_table_mc2_w_tax.biom --qualitative -o stats_OTUs_per_sample.txt

# Get number of reads per sample (not normalized OTU table)

biom summarize-table -i otu_table_mc2_w_tax.biom -o stats_reads_per_sample.txt

head -20 stats_reads_per_samples.txt # print top 20 lines

Num samples: 40

Num observations: 113869 (total number of OTU cluster)

Total count: 1436372 (total number of sequences)

Table density (fraction of non-zero values): 0.041

Counts/sample summary:

Min: 5123.0

Max: 51423.0

Median: 22415.0

Mean: 27632.043

Std. dev.: 5203.534

Sample Metadata Categories: None provided

Observation Metadata Categories: taxonomy

Counts/sample detail:

SampleA: 5123.0

SampleB: 5634.0

SampleC: 6192.0



Convert otu_table.biom to .tsv tab separated text file for using in Excel

# Convert .biom into .tsv text file (including taxa labels)

biom convert -i otu_table.biom -o otu_table.csv --to-tsv --header-key taxonomy

# Convert tab-separated .csv text file into .biom file

type "OTU table" requires last (empty) column "taxonomy"

biom convert -i otu_table.csv -o otu_table.biom --table-type="OTU table" --process-obs-metadata taxonomy --to-hdf5

How to edit .biom format files?

View biom-file on command line

biom head -i otu_table.biom

QIIME - filtering, splitting, and merging biom files

# example: remove all control samples from biom file (keep all '*' , but not '!' Control)

filter_samples_from_otu_table.py -i otu_table.biom -o otu_table_without_Control.biom -m mapfile.txt -s 'Treatment:*,!Control'

Python package



--> R package biomformat

read more

Biom file format



OTU table and .biom format