Quick Start

This is the minimal end-to-end run.

1) Make sure MAFFT works

From a terminal:

mafft --help

If MAFFT is not on your PATH, note the full path to the executable (or to mafft.bat on Windows).

2) Run the pipeline (CLI)

From the pipeline folder:

python HmtG-PacBio.py your_reads.fastq.gz

To control output location + prefix:

python HmtG-PacBio.py your_reads.fastq.gz --outdir results -o SampleA

3) Inspect outputs

In results/ you should see:

  • SampleA_report.pdf and SampleA_report.json

  • intermediate files (subsampled FASTQ/FASTA, MAFFT MSA)

  • haplotype FASTA files and distance tables

See Outputs for a detailed description.