| See also
Clusters sequences in a FASTA
or FASTQ file using a variant of the UCLUST algorithm designed to minimize memory
It's is the user's responsibility to sort the input
sequences in an appropriate order before running cluster_smallmem; see UCLUST sort order for
discussion. By default, input sequences are expected
to be sorted by decreasing length. If some other sort order is
used, the ‑sortedby option should be specified.
Valid values are length (default), size and other.
If -sortedby other is specified, then USEARCH does not assume or check for any
particular order. See also sortbysize and
threshold must be specified using the ‑id option.
Multithreading is not supported as this
would require significant memory overhead.
By default, nucleotide matching is done on the forward
strand only. For matching on both strands, use -strand both.
See search flowchart
for an overview of searching in USEARCH commands. Searching is used to match input
sequences to existing cluster centroids.
Standard output file
usearch -cluster_smallmem query.fasta -id 0.9
-centroids nr.fasta -uc clusters.uc