| 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 |
|
Greedy construction of OTUs. Used for
OTU
clustering of marker gene reads (obtained from mock or real environmental
samples). |
|
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 |
|
Masking |
|
Detection of repetitive or low-complexity
regions. |
|
Read quality filtering |
|
Quality filtering of reads in FASTQ format. |