Releases: marbl/verkko
verkko v1.0
These are release notes for Verkko version 1.0, which was released on April 18th, 2022. Verkko is a hybrid genome assembly pipeline developed for telomere-to-telomere assembly of PacBio HiFi and Oxford Nanopore 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
- coming soon
Minimum Requirements
- 8GB minimum memory; 16GB strongly suggested
- GCC 7 or newer (for compilation only)
- Rust 1.58 or newer (for compilation only)
- Python 3.5 or newer
- Snakemake 7.0 or newer
- GraphAligner v1.0.16 or newer
- MBG v1.0.10 or newer
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/v1.0/verkko-v1.0.tar.gz --output verkko-v1.0.tar.gz
tar -xzf verkko-v1.0.tar.gz
cd verkko-v1.0/src
make -j 8
cd ..
Confirm the MD5 for the tar.gz matches expected:
3cb085c0e015f01f61be67ee80da632c verkko-v1.0.tar.gz
Verkko will be installed in verkko-v1.0/bin. You can move the contents to verkko-v1.0/bin/* and verko-v1.0/lib/* to a central location if you would like. If GraphAligner or MBG are not available in your path, you may also symlink them under verkko/lib/verkko/bin/
See the README for more details.
Changes
- Added trio-based phasing (also supports Hi-C or Strand-Seq data), see the README for usage
- Updated GraphAligner to speed up ONT alignment and reduce memory usage
Bug Fixes
- Fix crash in MBG resolution (maickrau/MBG@0a61321)
- Fix slurm support in snakemake 7+ (8c37717)
- Fix consensus crashes due to reads >2 Mbp (marbl/canu@7041856)
- Fix consensus crashes due to over-trimming in contigs (marbl/canu@1a710da)
- Fix consensus bug that would prematurely terminate some contigs (marbl/canu@ce56a1e)
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.
verkko v1.0 beta2
These are release notes for Verkko version 1.0 beta2, which was released on February 25th, 2022. Verkko is a hybrid genome assembly pipeline developed for telomere-to-telomere assembly of PacBio HiFi and Oxford Nanopore reads.
The source code distribution contains everything you need to create a binary distribution for your own specific OS. This is a beta release so please report any issues you encounter.
Citation
- coming soon
Minimum Requirements
- 8GB minimum memory; 16GB strongly suggested
- GCC 7 or newer (for compilation only)
- Python 3.5 or newer
- Snakemake 6.0 or newer
- GraphAligner v1.0.15 or newer
- MBG v1.0.9 or newer
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/v1.0_beta2/verkko-v1.0.tar.gz --output verkko-v1.0.tar.gz
tar -xzf verkko-v1.0.tar.gz
cd verkko-v1.0/src
make -j 8
cd ..
Confirm the MD5 for the tar.gz matches expected:
f8b71dfbcfcdfa31fce5c14f75f41ef7 verkko-v1.0.tar.gz
Verkko will be installed in verkko-v1.0/bin. You can move the contents to verkko-v1.0/bin/* and verko-v1.0/lib/* to a central location if you would like. If GraphAligner or MBG are not available in your path, you may also symlink them under verkko/lib/verkko/bin/
See the README for more details.
Changes
- Updated MBG construction and initial resolution
- Added option to run w/o ONT data
- Clean up intermediate outputs to save space, can be disabled with --keep-intermediate
Bug Fixes
- Fix incorrect HiFi read correction (635d4af)
- Fix crashes with the dry-run option (9323e71)
- Abort immediately when invalid/missing HiFi reads are provided (1a00b60)
- Fix crashes on nodes w/o coverage (fd7725e)
- Fix crash building layouts (24e20b6)
- Fix crash on perfect palindrome k-mers (maickrau/MBG@d04c73b)
Known Issues
See the issues page for up-to date open issues, or to report a problem.
- Long runtime of MBG with very large coverage (>200x). We recommend downsampling to 100x.
- Long runtimes aligning ONT reads. Some genomes require 3-5 days for each aligment job. This will be addressed in a future release.
- 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.
verkko v1.0 beta
These are release notes for Verkko version 1.0 beta, which was released on January 20th, 2022. Verkko is a hybrid genome assembly pipeline developed for telomere-to-telomere assembly of PacBio HiFi and Oxford Nanopore reads.
The source code distribution contains everything you need to create a binary distribution for your own specific OS. This is a beta release so please report any issues you encounter.
Citation
- coming soon
Minimum Requirements
- 8GB minimum memory; 16GB strongly suggested
- GCC 7 or newer (for compilation only)
- Python 3.5 or newer
- Snakemake 6.0 or newer
- GraphAligner v1.0.14 or newer
- MBG v1.0.8 or newer
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/v1.0_beta/verkko-v1.0.tar.gz --output verkko-v1.0.tar.gz
tar -xzf verkko-v1.0.tar.gz
cd verkko-v1.0/src
make -j 8
cd ..
Confirm the MD5 for the tar.gz matches expected:
ae57ec883cafd846b84fcc5795949e34 verkko-v1.0.tar.gz
Verkko will be installed in verkko-v1.0/bin. You can move the contents to verkko-v1.0/bin/* and verko-v1.0/lib/* to a central location if you would like. If GraphAligner or MBG are not available in your path, you may also symlink them under verkko/lib/verkko/bin/
See the README for more details.
Legal
See the README.licenses file and individual source code files for details.