Verkko v2.3.1

These are release notes for Verkko version 2.3.1, which was released on March 6th, 2026. Verkko is a hybrid genome assembly pipeline developed for telomere-to-telomere assembly of accurate long reads (PacBio HiFi, Oxford Nanopore Duplex, HERRO or hifiasm corrected Oxford Nanopore Simplex) and Oxford Nanopore ultra-long reads.

The source code distribution contains everything you need to create a binary distribution for your own specific OS. Please report any issues you encounter.

Citation

• Rautiainen M, Nurk S, Walenz BP, Logsdon GA, Porubsky D, Rhie A, Eichler EE, Phillippy AM, Koren S. Telomere-to-telomere assembly of diploid chromosomes with Verkko. Nat Biotech. (2023). doi:10.1038/s41587-023-01662-6
• Antipov D, Rautiainen M, Nurk S, Walenz BP, Solar SJ, Phillippy AM, Koren S. Verkko2 integrates proximity ligation data with long-read De Bruijn graphs for efficient telomere-to-telomere genome assembly, phasing, and scaffolding. Genome Research (2025). doi:10.1101/gr.280383.124

Minimum Requirements

• 8GB minimum memory; 16GB strongly suggested
• GCC 9 or newer (for compilation only)
• Rust (v1.74+) (for compilation only)
• Python (v3.10+), with biopython, parasail, and networkx modules
• Snakemake >=7.0, <8.0
• bamtools >=2.5.2
• MashMap 2.0 or newer (for filtering known sequences and Hi-C)
• GraphAligner v1.0.19 or newer
• Winnowmap
• For Hi-C/PoreC phasing:
  • BWA (Hi-C only)
  • minimap2 (PoreC only)
  • samtools
  • seqtk
  • networkx(>=2.6)

Installation

Users can download Verkko as source code or installed through a package manager like conda. The source code package needs to be compiled and installed before it can be used. Do NOT download the .zip source code. It is missing files and will not compile. This is a known flaw with git itself.

Run either:

install from conda

conda install -c conda-forge -c bioconda -c defaults verkko

or build from source

curl -L https://github.com/marbl/verkko/releases/download/v2.3.1/verkko-v2.3.1.tar.gz --output verkko-v2.3.1.tar.gz
md5sum verkko-v2.3.1.tar.gz

Confirm the MD5 for the tar.gz matches expected: b8ed491696cedfbc9f48cf88fa7eebd8 verkko-v2.3.1.tar.gz and compile:

tar -xzf verkko-v2.3.1.tar.gz
cd verkko-v2.3.1/src
make -j 8
cd ..

Verkko will be installed in verkko-v2.3.1/bin. You can move the contents to verkko-v2.3.1/bin/* and verko-v2.3.1/lib/* to a central location if you would like. If GraphAligner, Winnowmap, MashMap, bwa, or samtools are not available in your path, you may also symlink them under verkko-v2.3.1/lib/verkko/bin/

See the README for more details.

Updates

Verkko v2.3.1 IS (expected to be) compatible with assemblies started with Verkko v2.3 but not any earlier version. We DO NOT recommend mixing versions.

• Output CRAM files rather than BAM to save space.

Bug Fixes

• Fix Slow consensus package build (#348)
• Fix various consensus bugs (#347, #350, #353)
• Fix handling of reads > 2 Mbp in consensus (#351)
• Full Changelog: v2.3...v2.3.1

Known Issues

See the issues page for up-to date open issues, or to report a problem.

• Long runtime of MBG and high disk usage in overlapping with very high HiFi coverage (>200x). We recommend downsampling to 100x.
• Prioritization of HiFi data over corrected ONT data for consensus is currently based on read name, assuming HiFi data starts with an 'm' and number indicating the instrument ID.
• CRAM output groups corrected ONT data and HiFi data into a single read group.

Legal

See the README.licenses file and individual source code files for details.