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  "Maintainer": "Cassandra Stamsaas <cassandra.stamsaas@nmbu.no>",
  "Description": "Processing and analysis of amplicon sequencing data, with\na primary focus on eDNA metabarcoding while remaining\napplicable to general targeted sequencing workflows. The\npackage provides a user-friendly interface for core 'VSEARCH'\n(Rognes et al. (2016), <doi:10.7717/peerj.2584>) functions,\nextended with dedicated tools for visualization and parameter\ntuning.",
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    "fastx_synchronize",
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    "plot_read_quality",
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    "vs_cluster_size",
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    "vs_cluster_unoise",
    "vs_fastq_join",
    "vs_fastq_mergepairs",
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    "vs_fastx_trim_filt",
    "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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        "fastq_combine_files",
        "fastx_combine_files"
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    },
    {
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      "title": "Synchronize FASTA and FASTQ files or objects",
      "topics": [
        "fasta_synchronize",
        "fastq_synchronize",
        "fastx_synchronize"
      ]
    },
    {
      "page": "make_sintax_db",
      "title": "Make Sintax database",
      "topics": [
        "make_sintax_db",
        "sintax_db"
      ]
    },
    {
      "page": "phyloseq2rsearch",
      "title": "Convert phyloseq object to Rsearch object",
      "topics": [
        "phyloseq2rsearch"
      ]
    },
    {
      "page": "plot_base_quality",
      "title": "Plot quality scores per position for FASTQ reads",
      "topics": [
        "plot_base_quality"
      ]
    },
    {
      "page": "plot_ee_rate_dist",
      "title": "Plot distribution of expected error (EE) rate of reads",
      "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"
      ]
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      "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"
      ]
    },
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      "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"
      ]
    },
    {
      "page": "vs_cluster_size",
      "title": "Cluster FASTA sequences",
      "topics": [
        "cluster",
        "cluster_size",
        "vs_cluster",
        "vs_cluster_size"
      ]
    },
    {
      "page": "vs_cluster_subseq",
      "title": "Cluster FASTA sequences",
      "topics": [
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        "vs_cluster_subseq"
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    },
    {
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      "title": "Denoising FASTA sequences",
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        "denoise",
        "unoise",
        "vs_cluster_unoise"
      ]
    },
    {
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      "title": "Join paired-end sequence reads",
      "topics": [
        "fastq_join",
        "join",
        "vs_fasta_join",
        "vs_fastq_join",
        "vs_fastx_join"
      ]
    },
    {
      "page": "vs_fastq_mergepairs",
      "title": "Merge paired-end sequence reads",
      "topics": [
        "fastq_mergepairs",
        "mergepairs",
        "vs_fasta_mergepairs",
        "vs_fastq_mergepairs",
        "vs_fastx_mergepairs",
        "vs_mergepairs"
      ]
    },
    {
      "page": "vs_fastx_subsample",
      "title": "Subsample sequences",
      "topics": [
        "fastx_subsample",
        "subsample",
        "vs_fasta_subsample",
        "vs_fastq_subsample",
        "vs_fastx_subsample",
        "vs_subsample"
      ]
    },
    {
      "page": "vs_fastx_trim_filt",
      "title": "Trim and/or filter sequences in FASTA/FASTQ format",
      "topics": [
        "fastx_trim_filt",
        "trim_filt",
        "vs_fasta_trim_filt",
        "vs_fastq_trim_filt",
        "vs_fastx_trim_filt"
      ]
    },
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      "title": "Dereplicate sequences",
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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"
      ]
    },
    {
      "page": "vs_merging_lengths",
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      "topics": [
        "merging_lengths",
        "vs_merging_lengths"
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    },
    {
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        "optimize_truncee_rate",
        "vs_optimize_truncee_rate"
      ]
    },
    {
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      "topics": [
        "optimize_truncqual",
        "vs_optimize_truncqual"
      ]
    },
    {
      "page": "vs_search_exact",
      "title": "Search for exact full-length matches",
      "topics": [
        "search_exact",
        "vs_search_exact"
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    },
    {
      "page": "vs_sintax",
      "title": "Taxonomic classification using the Sintax algorithm",
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        "classify",
        "sintax",
        "vs_sintax"
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      "title": "Detect chimeras without external references (i.e. de novo)",
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        "uchime_denovo",
        "vs_uchime_denovo"
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    },
    {
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        "vs_uchime_ref"
      ]
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      "topics": [
        "global_alignment",
        "usearch_global",
        "vs_usearch_global"
      ]
    },
    {
      "page": "vsearch",
      "title": "Test if 'VSEARCH' can be executed",
      "topics": [
        "vsearch"
      ]
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