usearch -cluster_fast seqs.fasta -id 0.9 -centroids nr.fasta
| | | |
| Command Input file Output file
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
Commands
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).
Options
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.