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USEARCH algorithms

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  Papers and citing USEARCH

Algorithm   Description
USEARCH   Ultra-fast global alignment search for high-identity top hit or hits.
UCLUST   Ultra-fast general-purpose clustering. See also OTU clustering.
UBLAST   Fast, sensitive database search by local alignment. Similar to BLAST in some ways, but much faster due to the use of an index.
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..
UCHIME2   Search for chimeric sequences.
Dereplication   Find unique sequences (delete duplicated sequences).
ORF detection   Identification of Open Reading Frames (ORFs) in nucleotide sequences.
Local clustering   Clustering using local alignments
Paired read merging   Merging (assembly) of paired reads.
UNOISE2   Error-correction (denoising) of amplicon reads
UTAX   Taxonomy prediction for marker genes (16S, ITS...). No longer supported.
SINTAX   Taxonomy prediction for marker genes (16S, ITS...).
Read quality filtering   Quality filtering of reads with Phred (quality) scores..
Masking   Detection of repetitive or low-complexity regions.
Demultiplexing   Assign reads to samples using index reads.
UNCROSS   Detect and filter cross-talk in a OTU table.
UNBIAS   Correct for amplification bias in an OTU table.