Haemo Mito Pipeline
A script-first bioinformatics pipeline for generating mitochondrial haplotypes from long-read amplicon data targeting ~6 kb haemosporidian mitochondrial genomes.
This software is developed and maintained by the Escalante–Pacheco Lab (Temple University) as part of our haemosporidian genomics toolkit.
This documentation site covers:
What the pipeline does (and what it does not do)
How to run it (CLI + optional desktop GUI)
How to interpret the outputs (PDF/JSON/FASTA/TSV)
The experimental protocol context (primer design + sequencing workflow)
Note
This pipeline is designed for research and biodiversity/population studies. It is not intended as a diagnostic workflow.
Pipeline overview
At a high level, the pipeline runs:
FASTQ → Q-filter + subsample (default: Q≥30, n=5000)
Subsample FASTA → MAFFT MSA (with orientation adjustment)
MSA + FASTQ → haplotypes/OTUs + report
(Optional) Local BLAST per haplotype against a user-provided reference DB
All-vs-all haplotype distance matrix
A simplified view of the main steps.
Parameters
Methods
Reference