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. |