Workflow & Tool Map

A comprehensive, à la carte map of Mycelia’s capabilities. Each row connects:

• Input data type (FASTQ/FASTA/GFA/BAM/VCF, etc.)
• Mycelia entry points (Julia functions)
• Wrapped third-party tools
• Outputs (assemblies, QC tables, summary results, taxonomic abundance tables, etc.)
• Tutorials that walk through the transformation

Planned capabilities are rendered in <span style="background-color:#f0f0f0;">shaded cells</span> so we can see what still needs to be built.

NOTE: If a workflow uses third-party tools or datasets, cite them. See References for citation guidance.

High-Level Data Flow (Mermaid)

flowchart LR
    subgraph Inputs
        FASTQ["FASTQ reads<br/>(Illumina/PacBio/Nanopore)"]
        FASTA["FASTA genomes / contigs / transcripts"]
        GFA["Assembly graphs<br/>(GFA / FASTG)"]
        BAM["Alignments<br/>(BAM / SAM / CRAM)"]
        VCF["Variants<br/>(VCF)"]
        REF["Reference genomes<br/>(NCBI / custom)"]
    end

    subgraph QC
        QCReads["Quality Control<br/>(fastp / filtlong / native QC)"]
        QCTables["QC tables<br/>+ HTML reports"]
    end

    subgraph Assembly
        Assemblers["Assemblers<br/>(MEGAHIT, metaSPAdes,<br/>Flye, hifiasm, Rhizomorph)"]
        GraphOps["Graph utilities<br/>(Rhizomorph / GFA I/O)"]
    end

    subgraph PostProc["Post-processing"]
        Validation["Assembly validation<br/>(QUAST, BUSCO, CheckM/CheckM2, MUMmer)"]
        Annotation["Gene annotation<br/>(Pyrodigal, BLAST+, MMSeqs2, tRNAscan-SE, TransTerm, MLST)"]
        Taxonomy["Taxonomic profiling<br/>(taxonomy utilities, planned Kraken-style wrappers)"]
        Pangenome["Pangenome & distance<br/>(Mash, pangenome graphs)"]
        Variants["Variant analysis<br/>(GATK / vcfeval / FreeBayes / Clair3 / BCFtools)"]
    end

    subgraph Outputs
        Tables["Summary & QC tables"]
        Abund["Taxonomic & functional abundance tables"]
        Graphs["Graphs<br/>(GFA / internal graph types)"]
        Reports["HTML / text reports & plots"]
    end

    FASTQ --> QCReads
    QCReads --> QCTables
    QCReads --> Assemblers
    FASTA --> Pangenome
    FASTA --> Assemblers
    GFA --> GraphOps
    GraphOps --> Assemblers
    Assemblers --> Validation
    Assemblers --> Annotation
    Assemblers --> Pangenome
    Assemblers --> Graphs

    BAM --> Validation
    BAM --> Variants
    BAM --> Taxonomy

    VCF --> Variants
    REF --> Variants
    REF --> Pangenome

    Validation --> Tables
    Annotation --> Tables
    Taxonomy --> Abund
    Pangenome --> Tables
    Pangenome --> Graphs
    Variants --> Tables
    QCTables --> Reports
    Tables --> Reports
    Abund --> Reports

Use this diagram as the “big picture”; the tables below are the detailed à la carte menu.

1. End-to-End Menu (by Input Type)

1.1 FASTQ / FASTA / GFA / BAM / VCF → Outputs

2. Capability Matrix (by Task)

This mirrors patch 2’s capability section and ensures everything is covered from a “what do I want to do?” perspective.

3. Module coverage & doc gaps

3.1 Auto-included modules (from src/Mycelia.jl)

These bullets are a concise, user-facing summary of the auto-included modules.

• Core graph + I/O: utility-functions.jl, alphabets.jl, constants.jl, fastx.jl, rhizomorph/rhizomorph.jl (core enums/evidence, fixed-length graphs, variable-length graphs, graph algorithms) → Exposed via Rhizomorph: build_ngram_graph, build_kmer_graph, build_qualmer_graph, build_fasta_graph, build_fastq_graph, path-finding & simplification utilities.
• Assembly pipelines: assembly.jl (external assemblers), iterative-assembly.jl (mycelia_iterative_assemble, improve_read_set_likelihood, find_optimal_sequence_path), viterbi-next.jl.
• Analytics & QC: quality-control-and-benchmarking.jl, performance-benchmarks.jl, kmer-analysis.jl, distance-metrics.jl.
• Taxonomy & annotation: taxonomy-and-trees.jl, classification.jl, reference-databases.jl, annotation.jl.
• Wrappers & orchestration: bioconda.jl, rclone.jl, slurm-sbatch.jl, neo4jl.jl, xam.jl.

3.2 External tool wrappers (no dedicated tutorials yet)

These wrappers are available in src/ but do not yet have dedicated tutorials. They are listed here so the function coverage map can point to an explicit doc location until tutorials are added.