Home Software Services About Contact     
 
Follow on twitter

Robert C. Edgar on twitter

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.

24-Nov-2016
UPARSE tutorial video posted on YouTube. Make OTUs from MiSeq reads.

 

USEARCH v11

otutab_group command

See also
  OTU table
  OTU commands
  Making an OTU table (otutab command)

Combines counts from sets of samples (groups). The input file must be in QIIME classic format.

Groups are specified in a group file, which is a tabbed text file given by the -labels option. Each line in the group file must have two fields: the sample identifier and the group identifier. Some samples may be omitted, and a sample may appear in more than one group. For example, the following group file specifies two groups, mock and soil, each with three samples.

Mock1    mock
Mock2    mock
Mock3    mock
Soil1    soil
Soil2    soil
Soil3    soil

The output file is specified by the -output option. The output file is also in QIIME classic format.

Example

usearch -otutab_group otutable.txt -labels groups.txt -output otutable_groups.txt