usearch12_documentation

Documentation for USEARCH v12

https://github.com/rcedgar/usearch12_documentation

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Documentation for USEARCH v12

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README.md

usearch12_manual

Documentation for USEARCH v12

To view as web site https://rcedgar.github.io/usearch12_documentation

Owner

Name: Robert Edgar
Login: rcedgar
Kind: user

Repositories: 4
Profile: https://github.com/rcedgar

Citation (citation.html)

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   allpairs_global command
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  <div>
   <a href="https://drive5.com/usearch">
    <img alt="USEARCH v12" src="usearch12_banner.jpg" style="position:absolute; top:40px; left:10px; padding:0px; border:0px;"/>
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      Commands
     </a>
     <br/>
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      Topics
     </a>
     <br/>
     <a class="SideButton" href="citation.html">
      Publications
     </a>
     <br/>
    </div>
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   <div class="ManText" style="left:20px; position: absolute; left:135px; width:695px; background-color:white; padding:10px">
    <h1>
     Publications
    </h1>
    <span class="paper_author">
     R.C. Edgar
    </span>
    <span class="paper_year">
     (2018),
    </span>
    <span class="paper_title">
     <span style="font-weight:bold">
      Taxonomy annotation and guide tree errors in 16S rRNA databases
     </span>
    </span>
    ,
    <span class="paper_link">
     <a href="https://doi.org/10.7717/peerj.5030">
      PeerJ 6:e5030
     </a>
    </span>
    <span class="paper_key">
     <br/>
     • Approx. one in five SILVA and Greengenes taxonomy annotations are wrong
    </span>
    <span class="paper_key">
     <br/>
     • SILVA and Greengenes trees have pervasive conflicts with type strain taxonomies
    </span>
    <br/>
    <br/>
    <span class="paper_author">
     R.C. Edgar
    </span>
    <span class="paper_year">
     (2018),
    </span>
    <span class="paper_title">
     <span style="font-weight:bold">
      Accuracy of taxonomy prediction for 16S rRNA and fungal ITS sequences
     </span>
    </span>
    ,
    <span class="paper_link">
     <a href="https://doi.org/10.7717/peerj.4652">
      PeerJ 6:e4652
     </a>
    </span>
    <span class="paper_key">
     <br/>
     • Cross-validation by identity, novel benchmark strategy enabling realistic accuracy estimates
    </span>
    <span class="paper_key">
     <br/>
     • Genus accuracy of best methods is 50% on V4 sequences
    </span>
    <span class="paper_key">
     <br/>
     • Recent algorithms do not improve on RDP Classifier or SINTAX
    </span>
    <br/>
    <br/>
    <span class="paper_author">
     R.C. Edgar and H. Flyvbjerg
    </span>
    <span class="paper_year">
     (2018),
    </span>
    <span class="paper_title">
     <span style="font-weight:bold">
      Octave plots for visualizing diversity of microbial OTUs
     </span>
    </span>
    ,
    <span class="paper_link">
     <a href="https://doi.org/10.1101/389833">
      https://doi.org/10.1101/389833
     </a>
    </span>
    <span class="paper_key">
     <br/>
     • Octave plots visualize alpha diversity as a histogram
    </span>
    <span class="paper_key">
     <br/>
     • Plots show shape and completeness of distribution
    </span>
    <br/>
    <br/>
    <span class="paper_author">
     R.C. Edgar
    </span>
    <span class="paper_year">
     (2018),
    </span>
    <span class="paper_title">
     <span style="font-weight:bold">
      UNCROSS2: identification of cross-talk in 16S rRNA OTU tables
     </span>
    </span>
    ,
    <span class="paper_link">
     <a href="https://doi.org/10.1101/400762">
      https://doi.org/10.1101/400762
     </a>
    </span>
    <span class="paper_key">
     <br/>
     • Cross-talk rate is approx. 1% in many Illumina datasets
    </span>
    <span class="paper_key">
     <br/>
     • Cross-talk can cause false positive core microbiome
    </span>
    <span class="paper_key">
     <br/>
     • UNCROSS2 algorithm for filtering cross-talk
    </span>
    <br/>
    <br/>
    <span class="paper_author">
     R.C. Edgar
    </span>
    <span class="paper_year">
     (2017),
    </span>
    <span class="paper_title">
     <span style="font-weight:bold">
      Accuracy of microbial community diversity estimated by closed- and open-reference OTUs
     </span>
    </span>
    ,
    <span class="paper_link">
     <a href="https://doi.org/10.7717/peerj.3889">
      PeerJ 5:e3889
     </a>
    </span>
    <span class="paper_key">
     <br/>
     • QIIME closed- and open-reference clustering generates huge numbers of spurious OTUs
    </span>
    <span class="paper_key">
     <br/>
     • Closed-reference OTU assignment splits strains and species even when no sequence errors
    </span>
    <span class="paper_key">
     <br/>
     • Closed-reference fails to assign different hyper-variable regions to the same OTU
    </span>
    <span class="paper_key">
     <br/>
     • Closed-reference discards many well-known species that are present in Greengenes
    </span>
    <br/>
    <br/>
    <span class="paper_author">
     R.C. Edgar
    </span>
    <span class="paper_year">
     (2017),
    </span>
    <span class="paper_title">
     <span style="font-weight:bold">
      SEARCH_16S: A new algorithm for identifying 16S ribosomal RNA genes in contigs and chromosomes
     </span>
    </span>
    ,
    <span class="paper_link">
     <a href="https://doi.org/10.1101/124131">
      https://doi.org/10.1101/124131
     </a>
    </span>
    <br/>
    <br/>
    <span class="paper_author">
     R.C. Edgar
    </span>
    <span class="paper_year">
     (2017),
    </span>
    <span class="paper_title">
     <span style="font-weight:bold">
      SINAPS: Prediction of microbial traits from marker gene sequences
     </span>
    </span>
    ,
    <span class="paper_link">
     <a href="https://doi.org/10.1101/124156">
      https://doi.org/10.1101/124156
     </a>
    </span>
    <br/>
    <br/>
    <span class="paper_author">
     R.C. Edgar
    </span>
    <span class="paper_year">
     (2017),
    </span>
    <span class="paper_title">
     <span style="font-weight:bold">
      "UNBIAS: An attempt to correct abundance bias in 16S sequencing, with limited success"
     </span>
    </span>
    ,
    <span class="paper_link">
     <a href="https://doi.org/10.1101/124149">
      https://doi.org/10.1101/124149
     </a>
    </span>
    <span class="paper_key">
     <br/>
     • Read abundance has very low correlation with species abundance
    </span>
    <span class="paper_key">
     <br/>
     • Bias caused by gene copy count variation and primer mismatches
    </span>
    <span class="paper_key">
     <br/>
     • Gene copy count and primer mismatches cannot be accurately predicted
    </span>
    <span class="paper_key">
     <br/>
     • Impossible to correct abundance bias
    </span>
    <br/>
    <br/>
    <span class="paper_author">
     R.C. Edgar
    </span>
    <span class="paper_year">
     (2017),
    </span>
    <span class="paper_title">
     <span style="font-weight:bold">
      Updating the 97% identity threshold for 16S ribosomal RNA OTUs
     </span>
    </span>
    ,
    <span class="paper_link">
     <a href="https://doi.org/10.1093/bioinformatics/bty113">
      Bioinformatics 34(14) 2371-2375
     </a>
    </span>
    <span class="paper_key">
     <br/>
     • Standard 97% OTU identity threshold is too low
    </span>
    <span class="paper_key">
     <br/>
     • Optimal OTU threshold is 99% for full-length 16S, 100% for V4
    </span>
    <br/>
    <br/>
    <span class="paper_author">
     R.C. Edgar
    </span>
    <span class="paper_year">
     (2016),
    </span>
    <span class="paper_title">
     <span style="font-weight:bold">
      UNCROSS: Filtering of high-frequency cross-talk in 16S amplicon reads
     </span>
    </span>
    ,
    <span class="paper_link">
     <a href="https://doi.org/10.1101/088666">
      https://doi.org/10.1101/088666
     </a>
    </span>
    <span class="paper_key">
     <br/>
     • Cross-talk is common, many are reads assigned to wrong sample
    </span>
    <span class="paper_key">
     <br/>
     • UNCROSS algorithm for filtering cross-talk
    </span>
    <br/>
    <br/>
    <span class="paper_author">
     R.C. Edgar
    </span>
    <span class="paper_year">
     (2016),
    </span>
    <span class="paper_title">
     <span style="font-weight:bold">
      UNOISE2: improved error-correction for Illumina 16S and ITS amplicon sequencing
     </span>
    </span>
    ,
    <span class="paper_link">
     <a href="https://doi.org/10.1101/081257">
      https://doi.org/10.1101/081257
     </a>
    </span>
    <span class="paper_key">
     <br/>
     • UNOISE2 algorithm, improved denoiser
    </span>
    <span class="paper_key">
     <br/>
     • Reduces false-positive chimeras compared to UNOISE and DADA2
    </span>
    <br/>
    <br/>
    <span class="paper_author">
     R.C. Edgar
    </span>
    <span class="paper_year">
     (2016),
    </span>
    <span class="paper_title">
     <span style="font-weight:bold">
      UCHIME2: improved chimera prediction for amplicon sequencing
     </span>
    </span>
    ,
    <span class="paper_link">
     <a href="https://doi.org/10.1101/074252">
      https://doi.org/10.1101/074252
     </a>
    </span>
    <span class="paper_key">
     <br/>
     • UCHIME2 algorithm, improved chimera detection
    </span>
    <span class="paper_key">
     <br/>
     • "Fake" chimeras are common, valid biological sequences matching two-parent model
    </span>
    <span class="paper_key">
     <br/>
     • Perfect chimera filtering impossible even with complete and correct reference
    </span>
    <span class="paper_key">
     <br/>
     • Realistic chimera benchmark
    </span>
    <br/>
    <br/>
    <span class="paper_author">
     R.C. Edgar
    </span>
    <span class="paper_year">
     (2016),
    </span>
    <span class="paper_title">
     <span style="font-weight:bold">
      SINTAX: a simple non-Bayesian taxonomy classifier for 16S and ITS sequences
     </span>
    </span>
    ,
    <span class="paper_link">
     <a href="https://doi.org/10.1101/074161">
      https://doi.org/10.1101/074161
     </a>
    </span>
    <span class="paper_key">
     <br/>
     • SINTAX taxonomy prediction algorithm
    </span>
    <span class="paper_key">
     <br/>
     • Fast and simple method, accuracy comparable to RDP Classifier
    </span>
    <br/>
    <br/>
    <span class="paper_author">
     R.C. Edgar and H. Flyvbjerg
    </span>
    <span class="paper_year">
     (2015),
    </span>
    <span class="paper_title">
     <span style="font-weight:bold">
      "Error filtering, pair assembly and error correction for next-generation sequencing reads"
     </span>
    </span>
    ,
    <span class="paper_link">
     <a href="https://doi.org/10.1093/bioinformatics/btv401">
      Bioinformatics 31(21) 3476-3482
     </a>
    </span>
    <span class="paper_key">
     <br/>
     • Quality filtering by expected errors
    </span>
    <span class="paper_key">
     <br/>
     • Bayesian paired read assembler
    </span>
    <span class="paper_key">
     <br/>
     • Most paired read assemblers calculate incorrect Q scores
    </span>
    <span class="paper_key">
     <br/>
     • UNOISE algorithm, first denoiser for Illumina reads
    </span>
    <br/>
    <br/>
    <span class="paper_author">
     R.C. Edgar
     <i>
      et al.
     </i>
    </span>
    <span class="paper_year">
     (2014),
    </span>
    <span class="paper_title">
     <span style="font-weight:bold">
      UCHIME improves sensitivity and speed of chimera detection
     </span>
    </span>
    ,
    <span class="paper_link">
     <a href="https://doi.org/10.1093/bioinformatics/btr381">
      Bioinformatics 27(16) 2194-2200
     </a>
    </span>
    <span class="paper_key">
     <br/>
     • Shows UCHIME faster and more accurate than ChimeraSlayer
    </span>
    <span class="paper_key">
     <br/>
     • This paper report misleading benchmark tests, see critique in UCHIME2 paper
    </span>
    <br/>
    <br/>
    <span class="paper_author">
     R.C. Edgar
    </span>
    <span class="paper_year">
     (2013),
    </span>
    <span class="paper_title">
     <span style="font-weight:bold">
      UPARSE: highly accurate OTU sequences from microbial amplicon reads
     </span>
    </span>
    ,
    <span class="paper_link">
     <a href="https://doi.org/10.1038/nmeth.2604">
      "Nat. Meth.  10, 996-998"
     </a>
    </span>
    <span class="paper_key">
     <br/>
     • Describes UPARSE algorithm for 97% OTU clustering
    </span>
    <span class="paper_key">
     <br/>
     • Stringent error filtering and discarding singletons necessary
    </span>
    <span class="paper_key">
     <br/>
     • Highly accurate OTUs from paired OTUs without full overlap
    </span>
    <br/>
    <br/>
    <span class="paper_author">
     R.C. Edgar
    </span>
    <span class="paper_year">
     (2010),
    </span>
    <span class="paper_title">
     <span style="font-weight:bold">
      Search and clustering orders of magnitude faster than BLAST
     </span>
    </span>
    ,
    <span class="paper_link">
     <a href="https://doi.org/10.1093/bioinformatics/btq461">
      Bioinformatics 26(19) 2460-2461
     </a>
    </span>
    <span class="paper_key">
     <br/>
     • USEARCH algorithm
    </span>
    <span class="paper_key">
     <br/>
     • Default citation for USEARCH software
    </span>
    <br/>
    <br/>
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