Compute basic OTU table statistics, rarefy and summarize OTU tables by taxa using miccaΒΆ


This tutorial requires Single-end sequencing to be done.

The command tablestats reports a sample summary, an OTU summary and the rarefaction curves for the input OTU table:

micca tablestats -i otutable.txt -o tablestats

Inspecting the file tablestats/tablestats_samplesumm.txt you can see that the less abundant sample contains 9053 reads:

Sample Depth NOTU NSingle
Mw_03  9053  716  142
Mw_02  9947  760  166
Mw_12  10843 792  168
...    ...  ...   ...


Rarefaction curves can be inspected through tablestats/tablestats_rarecurve.txt and tablestats/tablestats_rarecurve_plot.png.

To compare different samples, the OTU table must be subsampled (rarefied) using the command tablerare. In this case we are interested in rarefy the table with the depth of the less abundant sample (Mw_03):

micca tablerare -i otutable.txt -o otutable_rare.txt -d 9053

Now we can summarize communities by their taxonomic composition. The tabletotax creates in the output directory a table for each taxonomic level (taxtable1.txt, ..., taxtableN.txt). OTU counts are summed together if they have the same taxonomy at the considered level.

micca tabletotax -i otutable_rare.txt -t taxa.txt -o taxtables

Finally, we can generate a relative abundance bar plot from generated taxa tables, using the command tablebar. In this case only the bar plot relative to the taxonomy level 2 (phylum) will be generated:

micca tablebar -i taxtables/taxtable2.txt -o taxtables/taxtable2.png