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  "Title": "Processing and Analyzing Amplicon Sequence Data",
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    "vs_cluster_unoise",
    "vs_fastq_join",
    "vs_fastq_mergepairs",
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    "vs_fastx_uniques",
    "vs_merging_lengths",
    "vs_optimize_truncee_rate",
    "vs_optimize_truncqual",
    "vs_search_exact",
    "vs_sintax",
    "vs_uchime_denovo",
    "vs_uchime_ref",
    "vs_usearch_global",
    "vsearch"
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      "page": "fastx_combine_files",
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        "fastq_combine_files",
        "fastx_combine_files"
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    },
    {
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        "fastq_synchronize",
        "fastx_synchronize"
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    },
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        "sintax_db"
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      "title": "Convert phyloseq object to Rsearch object",
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        "phyloseq2rsearch"
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    {
      "page": "plot_base_quality",
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      "topics": [
        "plot_base_quality"
      ]
    },
    {
      "page": "plot_ee_rate_dist",
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      "topics": [
        "plot_ee_rate_dist"
      ]
    },
    {
      "page": "plot_read_quality",
      "title": "Plot read length vs. read quality",
      "topics": [
        "plot_read_quality"
      ]
    },
    {
      "page": "plot_size_dist",
      "title": "Plot distribution of size values",
      "topics": [
        "plot_size_dist"
      ]
    },
    {
      "page": "rsearch_obj",
      "title": "Create Rsearch object",
      "topics": [
        "rsearch_obj"
      ]
    },
    {
      "page": "rsearch2phyloseq",
      "title": "Convert Rsearch object to phyloseq object",
      "topics": [
        "rsearch2phyloseq"
      ]
    },
    {
      "page": "set_vsearch_executable",
      "title": "Set the VSEARCH executable",
      "topics": [
        "set_vsearch_executable"
      ]
    },
    {
      "page": "taxonomy_distance",
      "title": "Creates a distance object based on taxonomy information.",
      "topics": [
        "taxonomy_distance"
      ]
    },
    {
      "page": "taxonomy_tree",
      "title": "Make a taxonomy tree",
      "topics": [
        "taxonomy_tree"
      ]
    },
    {
      "page": "vs_alignment_classification",
      "title": "Taxonomic classification with LCA",
      "topics": [
        "alignment_classification",
        "lca",
        "lca_classification",
        "vs_alignment_classification"
      ]
    },
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      "page": "vs_cluster_size",
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      "topics": [
        "cluster",
        "cluster_size",
        "vs_cluster",
        "vs_cluster_size"
      ]
    },
    {
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      "title": "Cluster FASTA sequences",
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        "vs_cluster_subseq"
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    },
    {
      "page": "vs_cluster_unoise",
      "title": "Denoising FASTA sequences",
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        "cluster_unoise",
        "denoise",
        "unoise",
        "vs_cluster_unoise"
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    },
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        "fastq_join",
        "join",
        "vs_fasta_join",
        "vs_fastq_join",
        "vs_fastx_join"
      ]
    },
    {
      "page": "vs_fastq_mergepairs",
      "title": "Merge paired-end sequence reads",
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        "mergepairs",
        "vs_fasta_mergepairs",
        "vs_fastq_mergepairs",
        "vs_fastx_mergepairs",
        "vs_mergepairs"
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    },
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        "fastx_subsample",
        "subsample",
        "vs_fasta_subsample",
        "vs_fastq_subsample",
        "vs_fastx_subsample",
        "vs_subsample"
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    {
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        "trim_filt",
        "vs_fasta_trim_filt",
        "vs_fastq_trim_filt",
        "vs_fastx_trim_filt"
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        "dereplicate",
        "fastx_uniques",
        "vs_fasta_dereplicate",
        "vs_fasta_uniques",
        "vs_fastq_dereplicate",
        "vs_fastq_uniques",
        "vs_fastx_dereplicate",
        "vs_fastx_uniques"
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