| 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. |