Skip to content

Verkko v2.2

Latest
Latest
Compare
Choose a tag to compare
@skoren skoren released this 31 Aug 00:05
· 11 commits to master since this release
v2.2
f25e36c

These are release notes for Verkko version 2.2, which was released on August 31th, 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/verkko-v2.2.tar.gz --output verkko-v2.2tar.gz
md5sum verkko-v2.2.tar.gz

Confirm the MD5 for the tar.gz matches expected: ac1ca419bfbfe82f0e5275eb981fc66e verkko-v2.2.tar.gz and compile:

tar -xzf verkko-v2.2.tar.gz
cd verkko-v2.2/src
make -j 8
cd ..

Verkko will be installed in verkko-v2.2/bin. You can move the contents to verkko-v2.2/bin/* and verko-v2.2/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/lib/verkko/bin/

See the README for more details.

Updates

  • HiC/PoreC scaffolding
  • Further improved Hi-C/PoreC phasing, fewer unassigned nodes and missing genes
  • Improved bubble detection and removal in genomes with uneven heterozygosity rates (#245)
  • Option to generate bam files specifying read alignments to the final assembly via the --consensus-bam option.
  • Add PBS support (#88)

Bug Fixes

  • Fix winnowmap flags to increase -I option to correct MAPQ estimates for larger genomes (#252)
  • Fix undected failures when pipes are used (b56c53c)
  • Fix LSF support (bba6f8d)
  • Fix invalid gap sizes while filling (9514bb5)
  • Fix incorrectly detecting repeat nodes (a7396a5)
  • Fix cnspath not propagating labels/haplotype partitions (#241, #260)
  • Fix crash in ONT resolution (7248729, #268)
  • Fix crash in consensus (#247,#266)

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