Releases: marbl/verkko
Verkko v2.2.1
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 humanoption to--screen-human-contaminatsto clarify usage - Output BAM files now include RG tag to state whether reads were input as
--hifior--nanoand 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
--cleanupremoving 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.
Verkko v2.2
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-v2.2.tar.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-bamoption. - 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.
Verkko v2.1
These are release notes for Verkko version 2.1, which was released on May 14th, 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 (v3.5+), 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/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/v2.1/verkko-v2.1.tar.gz --output verkko-v2.1.tar.gz
md5sum verkko-v2.1.tar.gz
Confirm the MD5 for the tar.gz matches expected: 9d0aba5ddd9d22aacb8692f30cedba7e verkko-v2.1.tar.gz and compile:
tar -xzf verkko-v2.1.tar.gz
cd verkko-v2.1/src
make -j 8
cd ..
Verkko will be installed in verkko-v2.1/bin. You can move the contents to verkko-v2.1/bin/* and verko-v2.1/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/lib/verkko/bin/
See the README for more details.
Updates
- Native support for PoreC phasing/scaffolding across rDNA arrays
- Improved rDNA scaffolding
- Improved Hi-C/PoreC phasing, fewer unassigned nodes and missing genes
- Improved rukki handling of large homozygous stretches
- Speed up alignTips step (#239)
- Allow scaffolding across arbitrary user-supplied sequence, see
--rdna-scaff-refoption
Bug Fixes
- Fix incorrect sorting of Hi-C/PoreC data (f1b43f1)
- Fix incorrect use of Hi-C mashmap identity (8780981)
- Fix crash with invalid gap sizes while filling (9514bb5)
- Fix incorrectly detecting invalid hapmer files (#240)
- Fix mixing HPC/non-HPC reads when
--no-correctionis supplied (fc890f7) - Fix crash for scaffolds where one of the pieces had no reads assigned (b47102c)
- Fix crash in Hi-C scaffolding (68af043)
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.
Verkko v2.0
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.
Verkko v1.4.1
These are release notes for Verkko version 1.4.1, which was released on August 9th, 2023. 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 9 or newer (for compilation only)
- Rust 1.58 or newer (for compilation only)
- Python 3.5 or newer, with biopython, parasail, and networkx modules
- Snakemake 7.0 or newer
- MashMap 2.0 or newer (for filtering known sequences and Hi-C)
- GraphAligner v1.0.17 or newer
- Winnowmap
- MBG v1.0.14 or newer
- BWA (for Hi-C phasing)
- samtools (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/v1.4.1/verkko-v1.4.1.tar.gz --output verkko-v1.4.1.tar.gz
tar -xzf verkko-v1.4.1.tar.gz
cd verkko-v1.4.1/src
make -j 8
cd ..
Confirm the MD5 for the tar.gz matches expected:
37299a7938c9806763586c2d386f38e8 verkko-v1.4.1.tar.gz
Verkko will be installed in verkko-v1.4.1/bin. You can move the contents to verkko-v1.4.1/bin/* and verko-v1.4.1/lib/* to a central location if you would like. If GraphAligner, MBG, 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.
Bug Fixes
- Properly handle ONT reads during Hi-C/paths consensus (#166, #174)
- Various resolution crashes (#162, #163, #164, #165, #175)
- Various Hi-C pipeline errors (#173)
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 v1.4
These are release notes for Verkko version 1.4, which was released on June 27rd, 2023. 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 9 or newer (for compilation only)
- Rust 1.58 or newer (for compilation only)
- Python 3.5 or newer, with parasail module
- Snakemake 7.0 or newer
- Mashmap 2.0 or newer (for filtering known sequences and HiC)
- GraphAligner v1.0.17 or newer
- WinnowMap
- MBG v1.0.14 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/v1.4/verkko-v1.4.tar.gz --output verkko-v1.4.tar.gz
tar -xzf verkko-v1.4.tar.gz
cd verkko-v1.4/src
make -j 8
cd ..
Confirm the MD5 for the tar.gz matches expected:
6cc9374d06c5150bf055c5667d81592e verkko-v1.4.tar.gz
Verkko will be installed in verkko-v1.4/bin. You can move the contents to verkko-v1.4/bin/* and verko-v1.4/lib/* to a central location if you would like. If GraphAligner, MBG, Winnowmap or mashmap are not available in your path, you may also symlink them under verkko/lib/verkko/bin/
See the README for more details.
Changes
- Beta support for Hi-C phasing integration, see the --hic1 and --hic2 options in the README and command line help for details.
- Improved performance on low-coverage (<50x HiFi/ONT) samples (lower switch/hamming error rates, more T2T contigs and scaffolds)
- Added --haploid option to more aggressively pop bubbles on samples which are expected to be homozygous.
Bug Fixes
- Avoid losing low-coverage long nodes when simplifying the graph
- Various MBG crashes (#126, #145, #130, #131, #146)
- Various pipeline errors (#147, #141)
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 v1.3.1
These are release notes for Verkko version 1.3.1, which was released on March 6rd, 2023. 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 7 or newer (for compilation only)
- Rust 1.58 or newer (for compilation only)
- Python 3.5 or newer, with parasail module
- Snakemake 7.0 or newer
- Mashmap 2.0 or newer (for filtering known sequences)
- GraphAligner v1.0.17 or newer
- MBG v1.0.14 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/v1.3.1/verkko-v1.3.1.tar.gz --output verkko-v1.3.1.tar.gz
tar -xzf verkko-v1.3.1.tar.gz
cd verkko-v1.3.1/src
make -j 8
cd ..
Confirm the MD5 for the tar.gz matches expected:
004bf1e1767f273c6d9622d4b11ef612 verkko-v1.3.1.tar.gz
Verkko will be installed in verkko-v1.3.1/bin. You can move the contents to verkko-v1.3.1/bin/* and verko-v1.3.1/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
- Filtering of human rDNA, mitochondrial genome and Epstein–Barr virus via option
--screen human(requires mashmap). Other contaminants can be filtered using--screen <label> </path/to/single/sequence.fasta>. All contigs matching a contaminant are removed fromassembly.fastaand placed in their own file. The exemplar contig is circularized and saved separately. - Reduce memory usage in MBG.
- Resolve haplotype gaps when HiFi reads are available but to fill the gap but aren't high enough accuracy or long enough to be included in the MBG graph.
- Improved GraphAligner mapping within simple-sequence repeats.
- Fix rukki resolution homogenizing paths when no/low marker information is available.
- Fix rukki to assign repeat tangles to their appropriate haplotypes, when possible.
Bug Fixes
-
Fix error in v1.3 where haplotype-aware assemblies (
--hap-kmers) would attempt to use an obsolete program and would fail with:./combineConsensus.sh: /software/lib/verkko/scripts/process_reads.py: not found. -
Extremely slow read correction overlap computation on some datasets was resolved by counting all k-mers instead of a subset.
-
Fix various MBG bugs (https://github.com/maickrau/MBG).
-
Stop when duplicate reads are input to avoid MBG crashes later (#126).
-
Fix incorrect phasing in case of tied ONT alignments.
Known Issues
See the issues page for up-to date open issues, or to report a problem.
- Loss of long sequences with low HiFi coverage (<35x total or < 15x/haplotype), addressed by commit 0268963 and will be fixed in the next release.
- 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 v1.3
These are release notes for Verkko version 1.3, which was released on March 5rd, 2023. 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 7 or newer (for compilation only)
- Rust 1.58 or newer (for compilation only)
- Python 3.5 or newer, with parasail module
- Snakemake 7.0 or newer
- Mashmap 2.0 or newer (for filtering known sequences)
- GraphAligner v1.0.17 or newer
- MBG v1.0.14 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/v1.3/verkko-v1.3.tar.gz --output verkko-v1.3.tar.gz
tar -xzf verkko-v1.3.tar.gz
cd verkko-v1.3/src
make -j 8
cd ..
Confirm the MD5 for the tar.gz matches expected:
0657abc847e3d554289d2a88a3fdf774 verkko-v1.3.tar.gz
Verkko will be installed in verkko-v1.3/bin. You can move the contents to verkko-v1.3/bin/* and verko-v1.3/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
- Filtering of human rDNA, mitochondrial genome and Epstein–Barr virus via option
--screen human(requires mashmap). Other contaminants can be filtered using--screen <label> </path/to/single/sequence.fasta>. All contigs matching a contaminant are removed fromassembly.fastaand placed in their own file. The exemplar contig is circularized and saved separately. - Reduce memory usage in MBG.
- Resolve haplotype gaps when HiFi reads are available but to fill the gap but aren't high enough accuracy or long enough to be included in the MBG graph.
- Improved GraphAligner mapping within simple-sequence repeats.
- Fix rukki resolution homogenizing paths when no/low marker information is available.
- Fix rukki to assign repeat tangles to their appropriate haplotypes, when possible.
Bug Fixes
- Extremely slow read correction overlap computation on some datasets was resolved by counting all k-mers instead of a subset.
- Fix various MBG bugs (https://github.com/maickrau/MBG).
- Stop when duplicate reads are input to avoid MBG crashes later (#126).
- Fix incorrect phasing in case of tied ONT alignments.
Known Issues
See the issues page for up-to date open issues, or to report a problem.
-
An error in
Snakefiles/7-combineConsensus.smwill cause ALL haplotype-aware assemblies (--hap-kmers) to fail with error:
./combineConsensus.sh: /software/lib/verkko/scripts/process_reads.py: not found
Version v1.3.1 fixes the error, or you can fix a v1.3 installation with:
cd /software/lib/verkko/scripts/ ; ln -s fasta_extract.py process_reads.py -
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 v1.2
These are release notes for Verkko version 1.2, which was released on October 31st, 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
- Rautiainen M, Nurk S, Walenz BP, Logsdon GA, Porubsky D, Rhie A, Eichler EE, Phillippy AM, Koren S. Verkko: telomere-to-telomere assembly of diploid chromosomes. bioRxiv. (2022).
doi:10.1101/2022.06.24.497523
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 v1.0.12 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/v1.2/verkko-v1.2.tar.gz --output verkko-v1.2.tar.gz
tar -xzf verkko-v1.2.tar.gz
cd verkko-v1.2/src
make -j 8
cd ..
Confirm the MD5 for the tar.gz matches expected:
2975d74b265e22f9748385b08269d709 verkko-v1.2.tar.gz
Verkko will be installed in verkko-v1.2/bin. You can move the contents to verkko-v1.2/bin/* and verko-v1.2/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
- Update MBG from version 1.0.10 to 1.0.12.
Bug Fixes
- Avoid creating 1bp nodes when breaking mis-assembiles (#99)
- Fix additional constraint checking in snakemake 7.1.1 (#95)
- Fix crash on zero-length reads (#94)
- Fix crashes in dry-run.
Known Issues
See the issues page for up-to date open issues, or to report a problem.
- GraphAligner misses mappings on genomes with large (>20kb) stretches of simple sequence GA-rich repeats (only seen in plants so far), as a workaround, increase the
--seed-max-lengthfrom the default of10000to100000(note this will increase runtime 2-3 fold). This will be addressed in a future release. - 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 v1.1
These are release notes for Verkko version 1.1, which was released on August 7th, 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
- Rautiainen M, Nurk S, Walenz BP, Logsdon GA, Porubsky D, Rhie A, Eichler EE, Phillippy AM, Koren S. Verkko: telomere-to-telomere assembly of diploid chromosomes. bioRxiv. (2022).
doi:10.1101/2022.06.24.497523
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/v1.1/verkko-v1.1.tar.gz --output verkko-v1.1.tar.gz
tar -xzf verkko-v1.1.tar.gz
cd verkko-v1.1/src
make -j 8
cd ..
Confirm the MD5 for the tar.gz matches expected:
f77269f394f2cff580d1af25de0fed6d verkko-v1.1.tar.gz
Verkko will be installed in verkko-v1.1/bin. You can move the contents to verkko-v1.1/bin/* and verko-v1.1/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
- Update consensus module and parameters to increase accuracy
- Reduce stringency of ONT coverage filter, prevents valid nodes from being removed during ONT resolution, improving continuity
Bug Fixes
- Fix crash in MBG construction (#63)
- Fix memory leak during consensus
- Fix bubble popping removing large (multi-Mbp) nodes
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.