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Getting started
Installation,
command line,
What's new in
v8 (yellow,
blue = enhanced/added
since v8.0).
Quick start: for BLAST users,
for CD-HIT users, for
USEARCH v7
users
32-bit and 64-bit binaries,
memory requirements
Algorithms
OTU clustering with
UPARSE
Algorithm overview, USEARCH,
UCLUST,
UBLAST, UCHIME,
NAST,
UTAX,
agglomerative clustering,
read mapping, read quality filtering,
whole genome
alignment,
PCR amplicon prediction,
sequence masking,
rarefaction,
file format conversions
Taxonomy confidence
Commands
All commands
Clustering and dereplication:
cluster_otus, cluster_fast,
cluster_smallmem,
derep_fulllength, derep_prefix
cluster_agg,
cluster_aggd,
cluster_edges
Database search:
usearch_global,
usearch_local ublast,
search_global, search_local,
search_exact,
search_pcr,
search_oligodb,
search_peptidedb
Indexed databases:
makeudb_usearch,
makeudb_ublast,
udbstats, udbinfo,
udb2fasta
Taxonomy assignment:
utax,
cluster_otus_utax
Chimera filtering and classification:
uchime_ref,
uparse_ref,
uchime_denovo
FASTA/Q file processing:
sortbylength, sortbysize,
fastx_getseq,
fastx_getseqs,
fastx_getsubseq,
fastx_revcomp,
fastx_subsample,
fastx_truncate, fastx_mask,
fastx_findorfs,
fasta_rarify,
fastx_split,
fasta_diversity
FASTQ file processing:
fastq_filter,
fastq_mergepairs,
fastq_chars,
fastq_stats,
fastq_join,
fastq_eestats
SAM file filtering and conversion:
sam_filter
Distance matrix and trees:
calc_distmx,
tree2distmx,
tree2clusters,
draw_tree
Command-line options
All options,
output files, accept options, termination options, databases,
indexing options,
patterns (spaced
seeds), compressed
alphabets, file formats,
multithreading
Support
Technical support, feature requests,
bugs, feedback and corrections,
old manuals,
Papers and citing USEARCH,
Consulting services
and custom algorithm development
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