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USEARCH algorithms

See also
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...). Obsolete.
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 .

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