Run from the CLI
Basic run
python HmtG-PacBio.py reads.fastq.gz
Choose output folder + sample name
python HmtG-PacBio.py reads.fastq.gz --outdir results -o Sample01
Quality filter + subsampling
The first stage filters reads by mean Q-score and then randomly subsamples.
Common knobs:
--min-meanq(default: 30)--sample(default: 5000)--seed(default: 420)
Example:
python HmtG-PacBio.py reads.fastq.gz --min-meanq 30 --sample 8000 --seed 123 -o Sample01 --outdir results
MAFFT settings
The pipeline runs MAFFT with orientation adjustment enabled.
--threads(default: 30)--mafft(default:mafft)
Example (explicit MAFFT path):
python HmtG-PacBio.py reads.fastq.gz --mafft /usr/local/bin/mafft --threads 8 -o Sample01 --outdir results
Re-running / overwriting
By default, intermediate files are re-used if present.
To force regeneration:
python HmtG-PacBio.py reads.fastq.gz --force -o Sample01 --outdir results