Clusters sequences in a FASTA or FASTQ file using a variant of the UCLUST algorithm designed to maximize speed by multi-threading. It can be much faster than cluster_fast, depending on the input data.
An identity threshold must be specified using the - id option .
Sequences are processed in the order they appear in the input file.
Reverse-complemented matching for nucleotide sequences using -strand both is not supported.
Size annotations may be generated and/or propagated by using the - sizein and/or - sizeout options.
Output files
Standard output files
are supported. Cluster centroids (representative sequences) are written to a FASTA file specified by the -
centroids
option. Consensus sequences are written to a FASTA file specified by -
consout
and multiple alignments are written to filenames derived from the -
msaout option
. Note that using -consout and -msaout may add significantly to the compute time and memory required for clustering. You can specify a directory to contain one FASTA file per cluster using the -
clusters
option.
Supported options
Accept options
Termination options
Indexing options
Masking options
Multithreading
Alignment parameters
Alignment heuristics
Example
usearch -cluster_fast query.fasta -id 0.9 -centroids nr.fasta -uc clusters.uc