Pangebin (WIP)

Checkout ISMB2025 branch.

git checkout ismb2025

---

activate env

source venv/bin/activate

1. preprocess input files

sample_id="SAMN16357463" unicycler="test/data/SAMN16357463/unicycler.gfa.gz skesa="test/data/SAMN16357463/skesa.gfa.gz" out_dir="test/data/SAMN16357463/out" thr="1"

python3 src/pangebin preprocess ${sample_id} ${unicycler} ${skesa} --outdir {out_dir} --thr {thr}

mixed_fasta="test/data/SAMN16357463/out/SAMN16357463.1.mix.fasta"

2. make pangenome graph using ${mixed_fasta}

(pggb ...) pangenome="test/data/SAMN16357463/out/SAMN16357463.1.pan.gfa" cp ${pggb_out} ${pangenome

3. make pan-assembly graph

pangenome="test/data/SAMN16357463/out/SAMN16357463.1.pan.gfa" skesa="test/data/SAMN16357463/out/SAMN16357463.1.s.gfa" unicycler="test/data/SAMN16357463/out/SAMN16357463.1.u.gfa" sample_id="SAMN16357463" out_dir="test/data/SAMN16357463/out/"

python3 src/pangebin panassembly $pangenome $skesa $unicycler ${sample_id} ${out_dir}