USEARCH binary filename
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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.



USEARCH binary filename

As distributed, the USEARCH binary file has a long name like this: usearch6.0.98_i86linux32. Fields in the name are explained in the table below.

Renaming the binary file
It can be tedious to type a hard-to-remember long name like usearch6.0.98_i86linux32. I recommend renaming the binary file to usearch. Under Linux and OSX, you can do this by using the mv command or by creating a symbolic link using the ln command. For example:

ln -s usearch6.0.98_i86linux32 usearch

Using a symbolic link has the advantage that the original name is preserved and will be shown by the ls -l command, e.g:

ls -l usearch
lrwxr-xr-x 1 robert admin 26 2012-07-19 08:55 usearch -> usearch6.0.98_i86linux32

Windows doesn't support symbolic links. You can use any of the usual methods for renaming a file.

Getting the USEARCH version
You can get build information with the -version command, e.g.:

usearch -version

Field   Comments
usearch   Self-explanatory.
6.0   Major and minor version number. Major versions have significant changes in features and may not be compatible with each other. Minor versions have few or no changes in features, but may have important bug fixes.
98   Revision control number. Changes in this number are usually due to bug fixes.
i86   Processor type, e.g. i86 is Intel.
linux   Platform, indicates the operating system and runtime environment, examples include linux, osx. win and cygwin.
32   32 or 64 to indicate use of 32-bit or 64-bit processor instruction sets. 32-bit builds can run on 32- or 64-bit processors and are limited to a maximum of 4Gb or less memory per process, depending on the operating system and amount of installed memory. 64-bit builds run only on 64-bit processors and have no restrictions on the amount of memory.