Skip to content

Verkko v2.0
Compare
Choose a tag to compare
@skoren skoren released this 08 Feb 14:29
· 253 commits to master since this release
v2.0
44d3697

These are release notes for Verkko version 2.0, which was released on February 8th, 2024. 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 11 or newer (for compilation only)
  • Rust (v1.71+) (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 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/v2.0/verkko-v2.0.tar.gz --output verkko-v2.0.tar.gz
md5sum verkko-v2.0.tar.gz

Confirm the MD5 for the tar.gz matches expected: be5b322b2fcfcee07c0d64fa49c6a9b4 verkko-v2.0.tar.gz and compile:

tar -xzf verkko-v2.0.tar.gz
cd verkko-v2.0/src
make -j 8
cd ..

Verkko will be installed in verkko-v2.0/bin. You can move the contents to verkko-v2.0/bin/* and verko-v2.0/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

  • New overlapper module which is significantly faster than the previous version
  • Scaffolding across recognized rDNA arrays using Hi-C data
  • New GraphAligner tuned to respect haplotype differences and prefer haplotype-consistent paths
  • Improved repeat resolution in regions w/coverage differing from the global average
  • Improve handling of telomere ends

Bug Fixes

  • Scale reads used for each batch during read correction rather than using a fixed number which overflowed memory (#220)
  • Fix crash unrolling simple loops (#212)
  • Fix crash in processGraph (44d3697)
  • Fix crash in consensus going out of bounds (marbl/canu@6a0d004)
  • Fix screen option to convert paths to absolute rather than relative (#206)

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.

Assets 3
Loading