verkko
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marbl
In a primate sample (siamang) using verkko v1.4, we end up with a bubble structure  where there are two alternate 100kb nodes...
Hi, our local slurm cluster is configured in such a way that additional parameters are required when submitting jobs, and the job ID may contain a semicolon. This commit enables...
split coverage of a repetitive node to it's multiple copies. That may allow to simplify tangles better, distinguishing real low covered nodes from repeats.
When there is no trio data available, is it possible to produce hifiasm style pseudo-haplotype resolved assemblies? I was not able to produce the pseudo-haplotypes from the final assembly. Do...
Running verkko in trio mode, and failing on the createLayout step due to insufficient memory, but snakemake doesn't try to request more memory for the second job, and then fails...
Identify regions where the haplotypes only differ by homopolymers count and so are invisible in compressed space. These are likely to cause consensus issues when the two haplotypes are mixed...
``` verkko \ --paths some.gaf \ --assembly some-assembly \ -d some-output \ --hifi hifi/*fastq.gz ``` will fail to include ONT reads even if they exist in `some-assembly` because 7-buildPackages.sm sets...
- use extension smk instead of sm for syntax highlights on GitHub - check the new feature that supports using existing bash scripts rather than inlining them in the smk...
I saw there is support for SGE, Slurm and LSF; but does it also work for PBS submission systems?
Right now, we do not split reads so the full ONT reads are included even if the patch is much shorter. This can lead to issues when the patch is...