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USEARCH command line
A typical USEARCH command line looks like this:
usearch -cluster_fast seqs.fasta -id 0.9 -centroids nr.fasta
    |         |           |                   |        |
    |       Command   Input filename       Output option and filename
    Binary filename

The command line starts with the binary filename. In this manual, examples are always shown using 'usearch' as the filename. You should use the actual name of your binary file. You can rename your binary file to usearch or use the original name, e.g. usearch6.0.98_i86linux32.

The binary file must be in a directory in your shell's PATH variable, otherwise you must type the full path name, e.g. (Linux or OSX):

/usr/bin/usearch -cluster_fast seqs.fasta -id 0.9 -centroids nr.fasta

Under Windows, use backslashes and drive letters as needed:

C:\binaries\usearch.exe -cluster_fast seqs.fasta -id 0.9 -centroids nr.fasta

If the binary is in your current directory, you can use ./ or .\ (dot-slash or dot-backslash) as the path name:

./usearch -cluster_fast seqs.fasta -id 0.9 -centroids nr.fasta

A command line must have exactly one command. The command name is usually followed by the name of an input or query file in FASTA or FASTQ format (the format is automatically determined).

The USEARCH command-line must have one command and may have other options. An option is given after a hyphen (-). Command names are options, so must also have a hyphen. Two hyphens are allowed (Linux long option form), so both ‑id 0.9 and --id 0.9 are allowed. There must be a space between the option name and its value, so -id0.9 is not allowed.

Unused option warning
If a command-line option was not used by the given command, a warning message is issued.