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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.



problems installing and running USEARCH

See also: Installing USEARCH.

Missing DLL problem in Windows
See here if you get missing a vcomp100.dll error.

Permission denied error
The binary file must have read and execute permissions set. Use the chmod command to set the execute bit, e.g.:

  chmod a+rx /usr/bin/usearch6.0.98_i86linux32

Command not found error
If you get a command not found error or similar, then the executable file isn't in your path. The most common mistake people make is to put the program in the current directory when the current directory isn't in the path. To see the path under a shell, use:

  echo $PATH

If you're using a Windows command prompt, just type the PATH command:


The current directory is represented by a period. To run a command from the current directory when there is no period in the path, you can use something like:

  ./usearch6.0.98_i86linux32 -cluster seqs.fasta -id 0.9 -uc results.uc

Notice the dot and slash at the beginning of the line, this says run usearch from the current directory. If you don't know how to update your path, you can always use the full path name starting from the root (/), e.g.:

  /usr/bin/usearch6.0.98_i86linux32 -cluster seqs.fasta -id 0.9 -uc results.uc

Under the Windows command prompt, use back-slashes: