Introduction

What is this pipeline?

The Haemo Mito Pipeline is a small, practical workflow developed by the Escalante–Pacheco Lab (Temple University) to turn long-read amplicon data (targeting a ~6 kb haemosporidian mitochondrial genome region) into:

  • A curated set of mitochondrial haplotypes (FASTA)

  • Summary tables (TSV)

  • A human-readable PDF report

  • A machine-readable JSON report

The workflow follows the general strategy described in our published PacBio HiFi protocol and its companion HmtG-PacBio-style analysis approach.

What it is not

  • It is not a diagnostic assay.

  • It is not a full metagenomic assembler.

  • It does not attempt to delimit species automatically based on BLAST hits.

Instead, the idea is to provide a reproducible way to explore mixed infections / co-infections and to compare recovered haplotypes to a user-managed reference set.

Inputs and outputs at a glance

Input

  • FASTQ (optionally gzipped)

Outputs (prefix-based)

  • <prefix>_report.pdf and <prefix>_report.json

  • Haplotype FASTA outputs (high-frequency, low-frequency, chimeras)

  • Optional <prefix>_blast.tsv if BLAST is available

  • <prefix>_hapDistances.tsv all-vs-all distances

See Outputs for details.