USEARCH manual > command line |
USEARCH command line |
A typical USEARCH command line looks like this:
usearch -cluster_fast seqs.fasta -id 0.9 -centroids nr.fasta
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| 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 Command-line options Commands |