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USEARCH algorithms


Algorithm   Description
USEARCH   Ultra-fast search for high-identity top hit or hits.
UCLUST   Ultra-fast general-purpose clustering. See also OTU clustering.
UBLAST   Fast, sensitive database search.
UPARSE-REF   Error inference by maximum parsimony. Used for annotating sequences obtained in mock community experiments.
UPARSE-OTU   OTU clustering of marker gene reads, e.g. 16S or ITS..
UCHIME   Search for chimeric sequences.
Dereplication   Removal of duplicated sequences.
ORF detection   Identification of Open Reading Frames (ORFs) in nucleotide sequences.
Local clustering   Clustering using local alignments
TODO   Merging (assembly) of paired reads.
TODO: UNOISE   Denoising of amplicon reads
UTAX   Ultra-fast taxonomy assignment
Read quality filtering   Quality filtering of reads in FASTQ format.
Masking   Detection of repetitive or low-complexity regions.