✨ Highlights

🐟 verkko-fillet

Post-Verkko graph & assembly cleaning, in Python.

PyPI License Issues

verkko-fillet is a Python toolkit for cleaning, fixing, and gap-filling assemblies produced by the Verkko assembler. It bridges the gap between a raw Verkko run and a polished, chromosome-assigned, T2T-ready consensus.

Designed to be used interactively in Jupyter notebooks, it provides everything needed to QC the graph, assign chromosomes, recover broken contigs, fill gaps, and emit a corrected GAF path file ready for a Verkko consensus (CNS) run.

✨ Highlights#

  • 🧬 Quality control out of the box — N50, completeness, contig length, T2T status, chromosome coverage, and T2T QC plots.

  • 🗺️ Chromosome assignment — assign reference chromosomes and rename contigs based on a user-provided reference.

  • 🧩 Gap filling & path repair — detect, connect, and fill gaps and write back a fixed GAF for building new consensus.

  • 🧪 T2T QC — detect internal telomeres for trimming, summarize per-contig telomere percentages at chromosome ends, and visualize them.

  • 🔁 Reproducible — every step is recorded on the VerkkoFillet object with timestamp.

News#

🎉 v0.1.24 released#

A small maintenance release with debugging and reliability improvements to getChrNames.sh:

  • The neighborhood executable bundled alongside the script is now picked up automatically — no manual install required.

📄 Full changelog: v0.1.24

🎉 v0.1.23 released#

The latest release of verkko-fillet is out, with a new automated preprocessing CLI, gzipped FASTA support across the chromosome-renaming pipeline, mashmap caching, plotting improvements (PDF by default, force overwrite, tighter layouts), and several QoL fixes.

  • 📄 Full changelog: v0.1.23

  • 🆕 New tutorial: Automatic Preprocessing — run the standard QC + chromosome-assignment + telomere pipeline end-to-end with a single command.

We strongly recommend upgrading to the latest version for refining and cleaning Verkko assemblies.

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