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
Index
Index