somatem-docs/tools_keywords.json at main · treangenlab/somatem-docs · GitHub

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{
    "Centrifuge": [
        "short-read classification",
        "whole-genome shotgun"
    ],
    "Emu": [
        "full-length 16S rRNA",
        "long-read sequencing",
        "species-level resolution",
        "taxonomic abundance"
    ],
    "Sylph": [
        "low-abundance detection",
        "strain-level profiling"
    ],
    "Lemur": [
        "marker gene",
        "long-read profiling",
        "false positive reduction",
        "portable sequencing"
    ],
    "Magnet": [
        "whole-genome mapping",
        "long-read shotgun",
        "bacterial genome detection"
    ],
    "SeqScreen": [
        "pathogen characterization",
        "functional annotation",
        "synthetic DNA screening"
    ],
    "EggNog-mapper": [
        "functional annotation",
        "orthology assignment",
        "gene prediction",
        "protein domain discovery"
    ],
    "Rhea": [
        "structural variant detection",
        "strain-level resolution",
        "reference-free analysis"
    ],
    "Bakdrive": [
        "driver species",
        "ecological networks",
        "control theory",
        "host-specific variation",
        "microbiome restoration"
    ],
    "Apollo": [
        "genome annotation"
    ],
    "Flye": [
        "metagenomic datasets",
        "intra-species heterogeneity",
        "high contiguity",
        "biosynthetic gene clusters"
    ],
    "Chopper": [
        "Oxford Nanopore",
        "PacBio support"
    ],
    "Hostile": [
        "host read removal",
        "decontamination",
        "high precision filtering",
        "human-microbial separation"
    ],
    "Canu": [
        "de novo assembly",
        "noisy long reads",
        "adaptive overlapping"
    ],
    "NanoPlot": [
        "quality assessment",
        "phased alignment"
    ],
    "Parsnp": [
        "multiple genome alignment",
        "core-genome analysis",
        "bacterial genomes"
    ],
    "tMHG-Finder": [
        "maximal homologous groups",
        "guide tree scaling",
        "evolutionary analysis",
        "phylogenomic comparison"
    ],
    "AutoCycler": [
        "consensus assembly",
        "structural accuracy",
        "Oxford Nanopore"
    ]
}