| |
usearch_global |
|
Very fast search for high-identity top hit or
hits (global alignments). |
| |
usearch_local |
|
Very fast search for high-identity top hit or
hits (local alignments). |
| |
ublast |
|
Fast and sensitive search to low identities
(local alignments). |
| |
search_global |
|
Comprehensive search (global
alignments). |
| |
search_local |
|
Comprehensive search (local
alignments). |
| |
cluster_fast |
|
Clustering optimized for speed. |
| |
cluster_smallmem |
|
Clustering optimized for reduced memory
use. |
| |
cluster_otus |
|
Cluster marker gene sequences (e.g. 16S or ITS) into OTUs. |
| |
derep_fulllength |
|
Remove duplicated sequences (full-length
matches). |
| |
maskfasta |
|
Mask low-complexity regions. |
| |
derep_fulllength |
|
Remove duplicated sequences (full-length
matches). |
| |
derep_prefix |
|
Remove duplicated sequences (prefix
matches). |
| |
uchime_ref |
|
Chimera filter amplicon sequences using reference
database. |
| |
uchime_denovo |
|
Chimera filter amplicon reads de
novo. |
| |
pairs_local |
|
Align consecutive pairs 1&2,
3&4 ... N-1&N (local). |
| |
pairs_global |
|
Align consecutive pairs 1&2,
3&4 ... N-1&N (global). |
| |
allpairs_local |
|
Pairwise align all vs. all
(local). |
| |
allpairs_global |
|
Pairwise align all vs. all
(global). |
| |
sortbylength |
|
Sort sequences by decreasing
length. |
| |
sortbysize |
|
Sort sequences by decreasing size=N; value in
label. |
| |
makeudb_usearch |
|
Create a UDB database from a FASTA
file for usearch commands. |
| |
makeudb_ublast |
|
Create a UDB database from a FASTA
file for ublast command. |
| |
udb2fasta |
|
Convert UDB database to FASTA. |
| |
udbinfo |
|
Report UDB file header
information. |
| |
udbstats |
|
Report UDB index statistics. |
| |
findorfs |
|
Find open reading frames (ORFs) in nucleotide
sequences. |
| |
fastq_chars |
|
Report statistics on FASTQ quality scores. |
| |
fastq_filter |
|
Quality filter and / or convert FASTQ to FASTA. |
| |
fastq_mergepairs |
|
Merge overlapped paired reads into single reads. |
| |
version |
|
Show USEARCH build name with version and
platform. |
