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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.



Memory use and 32-/64-bit binaries

See also
  Memory requirements

USEARCH is distributed as a 32-bit or 64-bit binary file, also called an executable file.

32-bit binaries
A 32-bit binary is compatible with both 32-bit and 64-bit platforms, but is limited to using 4Gb or less memory. The 32-bit version is licensed at no charge.

64-bit binaries
A 64-bit binary requires a fully 64-bit platform (both processor and operating system), and can use all available physical memory. The 64-bit version requires a paid license.

Binary Free
32-bit CPU 64-bit CPU 32-bit O/S 64-bit O/S Maximum memory
32-bit Yes OK OK OK OK 4Gb (Linux, OSX)
2Gb (Windows)
64-bit No Not supported Required Not supported Required Can use all installed RAM

Finding the USEARCH binary type
As distributed, the binary file name indicates the platform. The version command can be used to determine the platform if the file has been renamed.

Finding the processor and O/S type
Under Linux and OSX, the uname -m command shows the processor. On an Intel or Intel-compatible platform (required by USEARCH) it will report x86_64 for a 64-bit processor and something without _x64, e.g. i686, for a 32-bit processor. Under Windows, you can right-click on Computer and select Properties. Under System, you should see information about the processor and O/S type: