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Verkko v2.2.1

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@skoren skoren released this 02 Oct 16:56
· 6 commits to master since this release
v2.2.1
0ffbc34

These are release notes for Verkko version 2.2.1, which was released on October 2nd, 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 (v3.10+), 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/v2.2.1/verkko-v2.2.1.tar.gz --output verkko-v2.2.1.tar.gz
md5sum verkko-v2.2.1.tar.gz

Confirm the MD5 for the tar.gz matches expected: d211ccb594cf0d60944ba92c9cbe33e9 verkko-v2.2.1.tar.gz and compile:

tar -xzf verkko-v2.2.1.tar.gz
cd verkko-v2.2.1/src
make -j 8
cd ..

Verkko will be installed in verkko-v2.2.1/bin. You can move the contents to verkko-v2.2.1/bin/* and verko-v2.2.1/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-v2.2.1/lib/verkko/bin/

See the README for more details.

Updates

Verkko v2.2.1 IS (expected to be) compatible with assemblies started with Verkko v2.2 but NOT with any earlier version. However, we DO NOT recommend mixing versions.

  • Update -screen human option to --screen-human-contaminats to clarify usage
  • Output BAM files now include RG tag to state whether reads were input as --hifi or --nano and whether they were used to patch gaps
  • Output BAM files now use final sequence names rather than intermediates

Bug Fixes

  • Fix missed scaffolds due to orientation (55e9c6e)
  • Fix --cleanup removing files too early (4d75aa0)
  • Fix drop in QV value due to changes to trimming, trimming is only skipped on large nodes or ends of scaffolds (to avoid removing telomere) (40388bc)
  • Fix build on OSX (5c1d50e)
  • Speed ups for layout and Hi-C scaffolding (33c2079, 4190b3c)

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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