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USEARCH manual
 
 
 
 
 
 

 
Getting started
What's new in v7
 
  Installation
    32-bit and 64-bit binaries, memory requirements
Command line
Quick start
   for BLAST users, for CD-HIT users
Understanding the algorithms
    USEARCH, UPARSE, UCLUST, UBLAST, UCHIME
 
Commands  All commands
Clustering and dereplication:
    cluster_otus, cluster_fast, cluster_smallmem,
    derep_fullength, derep_prefix
Database search:
    usearch_global, ublast, search_global, search_local
Chimera filtering and classification:
    uchime_ref, uparse_ref, uchime_denovo
FASTQ file processing:
    fastq_filter, fastq_mergepairs, fastq_chars, fastq_stats

Other:
    makeudb_usearch, makeudb_ublast, findorfs,
    maskfasta, sortbylength, sortbysize
 
 
Options   Options by category
    databases, output files, accept options, termination options,
    indexing options, patterns (spaced seeds),
    compressed alphabets, file formats, multithreading
   
Support   Technical support, feature requests, feedback and corrections
Consulting services and custom algorithm development

 
More   Old manuals
Papers and citing USEARCH
Benchmarks and performance