verkko v1.0 beta
Pre-release
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.