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Verkko v1.4.1
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@brianwalenz brianwalenz released this 09 Aug 17:00
· 351 commits to master since this release
v1.4.1
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These are release notes for Verkko version 1.4.1, which was released on August 9th, 2023. Verkko is a hybrid genome assembly pipeline developed for telomere-to-telomere assembly of accurate long reads (PacBio HiFi or Oxford Nanopore Duplex) 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 1.58 or newer (for compilation only)
  • Python 3.5 or newer, with biopython, parasail, and networkx modules
  • Snakemake 7.0 or newer
  • MashMap 2.0 or newer (for filtering known sequences and Hi-C)
  • GraphAligner v1.0.17 or newer
  • Winnowmap
  • MBG v1.0.14 or newer
  • BWA (for Hi-C phasing)
  • samtools (for Hi-C 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:

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

or build from source

curl -L https://github.com/marbl/verkko/releases/download/v1.4.1/verkko-v1.4.1.tar.gz --output verkko-v1.4.1.tar.gz
tar -xzf verkko-v1.4.1.tar.gz
cd verkko-v1.4.1/src
make -j 8
cd ..

Confirm the MD5 for the tar.gz matches expected:

37299a7938c9806763586c2d386f38e8  verkko-v1.4.1.tar.gz

Verkko will be installed in verkko-v1.4.1/bin. You can move the contents to verkko-v1.4.1/bin/* and verko-v1.4.1/lib/* to a central location if you would like. If GraphAligner, MBG, 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.

Bug Fixes

  • Properly handle ONT reads during Hi-C/paths consensus (#166, #174)
  • Various resolution crashes (#162, #163, #164, #165, #175)
  • Various Hi-C pipeline errors (#173)

Known Issues

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

  • Long runtime of MBG 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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