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Welcome

  • Introduction
    • What is this pipeline?
    • What it is not
    • Inputs and outputs at a glance
  • Installation
    • Requirements
    • Python dependencies (core)
    • MAFFT
    • BLAST (optional)
    • Build the docs locally (this website)
  • Quick Start
    • 1) Make sure MAFFT works
    • 2) Run the pipeline (CLI)
    • 3) Inspect outputs
  • Downloads
    • Windows Desktop GUI
    • macOS Desktop GUI
    • CLI workflow
    • Data + database downloads
    • Update these placeholders
  • About the lab
    • Contact and links

Tutorials

  • Tutorials
  • Run from the CLI
    • Basic run
    • Choose output folder + sample name
    • Quality filter + subsampling
    • MAFFT settings
    • Re-running / overwriting
  • Run from the GUI
    • Basic panel
    • Advanced panel (collapsible)
    • Recommended folder layout (project-local tools)
  • Using local BLAST
    • What BLAST is used for (in this workflow)
    • Install BLAST+
    • Prepare a database
    • Run and verify
  • Interpreting results
    • The PDF report
    • FASTA outputs
    • JSON report

Parameters

  • Essential parameters
    • Input
    • Output naming
    • Read filtering / subsampling
    • Alignment (MAFFT)
    • Reproducibility
  • Optional parameters
    • BLAST integration (optional)
    • Primer trimming/orientation
    • Advanced GUI-only toggles

Methods

  • Experimental protocol context
    • Target region
    • Primer design and multiplexing strategy
    • PCR overview (summary)
    • Sequencing
    • Recommended coverage (rule of thumb)
    • How this relates to the software
  • Pipeline design
    • Key components
    • Step-by-step (conceptual)
    • Why the pipeline is structured this way

Reference

  • Outputs
    • Main report artifacts
    • Haplotype FASTA outputs
    • BLAST output (optional)
    • Distances
    • Intermediate files
  • FAQ / Troubleshooting
    • MAFFT failed (return code 1) on Windows
    • BLAST table is missing
    • The PDF report is missing a figure
    • Where are my intermediate files?
  • Citation
    • Protocol paper
    • Software
    • External tools
  • Changelog
Haemo Mito Pipeline
  • Search

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