verkko
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marbl
Running verkko in `--paths` mode does not generate the same output files as a 'normal' run. The 'cnspath' rule does not create a `noseq.gfa` output - and probably others. This...
I'm attempting an assembly (relatively heterozygous diploid genome; 5Gb haploid size; with Hifi, ONT & Hi-C). In the directory 7-consensus, the uniting-popped fast = 7.3Gb; however the uniting.popped.haplotype1, haplotype2 and...
i.e. MissingInputException in rule alignBWA in file /data/antipovd2/devel/verkko/lib/verkko/Snakefiles/8-hicPipeline.sm, line 199: Missing input files for rule alignBWA: output: 8-hicPipeline/mapped002.bam wildcards: nnnn=002 affected files: 8-hicPipeline/split/hic2002.fasta.gz ERROR! Not running final consensus since no...
Hello, I recently updated my version of Snakemake to version 8, and now Verkko doesn't work. Specifically, I get the following error: ``` snakemake: error: unrecognized arguments: --reason ``` According...
Crashes are hard to find in current verkko log, also at some moment it would be nice to have more feedback like unoptimal parameters detected, or something went not how...
while hi-c jumping is not included we should not allow to use both hi-c and trio in the same run.
The GFA seem to have cigar string operations longer than either node. Also have 0M edges where we couldn't find the overlap post-consensus. Consider also updating the gfa to trim...
Currently, trio requires users to build homopolymer-compressed databases and we run one round of consensus after rukki resolution and coloring. In contrast, with Hi-C data, we run consensus, map Hi-C...
To simplify using trio-mode and not require running merqury separately.
I have two runs of HG002 with slightly different resolutions in the same genomic region with the same input data. The hifi graphs look similar, the new run: ![Screen Shot...