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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