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Verkko v2.1
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@skoren skoren released this 14 May 17:02
· 202 commits to master since this release
v2.1
932e872

These are release notes for Verkko version 2.1, which was released on May 14th, 2024. Verkko is a hybrid genome assembly pipeline developed for telomere-to-telomere assembly of accurate long reads (PacBio HiFi, Oxford Nanopore Duplex, HERRO 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

Minimum Requirements

  • 8GB minimum memory; 16GB strongly suggested
  • GCC 9 or newer (for compilation only)
  • Rust (v1.74+) (for compilation only)
  • Python (v3.5+), with biopython, parasail, and networkx modules
  • Snakemake >=7.0, <8.0
  • MashMap 2.0 or newer (for filtering known sequences and Hi-C)
  • GraphAligner v1.0.19 or newer
  • Winnowmap
  • For Hi-C/PoreC phasing:

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/v2.1/verkko-v2.1.tar.gz --output verkko-v2.1.tar.gz
md5sum verkko-v2.1.tar.gz

Confirm the MD5 for the tar.gz matches expected: 9d0aba5ddd9d22aacb8692f30cedba7e verkko-v2.1.tar.gz and compile:

tar -xzf verkko-v2.1.tar.gz
cd verkko-v2.1/src
make -j 8
cd ..

Verkko will be installed in verkko-v2.1/bin. You can move the contents to verkko-v2.1/bin/* and verko-v2.1/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/lib/verkko/bin/

See the README for more details.

Updates

  • Native support for PoreC phasing/scaffolding across rDNA arrays
  • Improved rDNA scaffolding
  • Improved Hi-C/PoreC phasing, fewer unassigned nodes and missing genes
  • Improved rukki handling of large homozygous stretches
  • Speed up alignTips step (#239)
  • Allow scaffolding across arbitrary user-supplied sequence, see --rdna-scaff-ref option

Bug Fixes

  • Fix incorrect sorting of Hi-C/PoreC data (f1b43f1)
  • Fix incorrect use of Hi-C mashmap identity (8780981)
  • Fix crash with invalid gap sizes while filling (9514bb5)
  • Fix incorrectly detecting invalid hapmer files (#240)
  • Fix mixing HPC/non-HPC reads when --no-correction is supplied (fc890f7)
  • Fix crash for scaffolds where one of the pieces had no reads assigned (b47102c)
  • Fix crash in Hi-C scaffolding (68af043)

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.
  • Lost heterozygosity in simple-sequence repeats in low-heterozygosity samples. When there is no other variation within at most 1 HiFi read length away, the simple sequence repeat difference will be ignored and a consensus of both haplotypes is produced. This will be addressed in a future release.

Legal

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

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