sintax_summary command
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11-Aug-2018 New paper describes octave plots for visualizing alpha diversity.

12-Jun-2018 New paper shows that one in five taxonomy annotations in SILVA and Greengenes are wrong.

18-Apr-2018 New paper shows that taxonomy prediction accuracy is <50% for V4 sequences.

05-Oct-2017 PeerJ paper shows low accuracy of closed- and open-ref. QIIME OTUs.

22-Sep-2017 New paper shows 97% threshold is wrong, OTUs should be 99% full-length 16S, 100% for V4.

UPARSE tutorial video posted on YouTube. Make OTUs from MiSeq reads.



sintax_summary command

ImageSee also
  sintax command

Creates a summary report for sintax predictions giving the frequencies of each named taxon at a given rank. For example, at phylum rank, the report might show 25% Bacteroidetes, 18% Firmicutes etc.

Input is an tabbed text output file from the sintax command (tabbedout option).

The rank option is required, it is a single letter specifying the rank, e.g. p for phylum. See taxonomy annotations for value letters.

An OTU table can be specified using the otutabin option. This will generate a report with frequencies for each sample and over all samples combined. The table must be in QIIME classic format. OTU identifiers in the OTU table must exactly match the labels in the sintax output file.

If size annotations are found in the sequence labels in the sintax output file, they are taken into account in calculating frequencies.

The output from sintax_summary can be imported into a spreadsheet or charting program for making figures.


usearch -sintax_summary sintax.txt -otutabin otutab.txt \
  -output phylum_summary.txt -rank p