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Hi, I get this error while trying to use AutoHiC latest version
RuntimeError: nms is not compiled with GPU support
Seems like it is related to mmcv/mmdet - I have tried every possible step tryi…
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Hi!! :)
I'm trying to run merqury but I can't obtain all the results. Could you help me please?
I'm following the steps:
# Step 1. Create meryl db:
`/opt/merqury-1.3/meryl count k=21 output /path…
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The pre- and post-yahs assemblies are identical. yahs runs fine but doesn't locate links between contigs because the bam file was sorted by position not read name, and yahs expects read pairs on subs…
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When starting an OTB run via `otb.sh ... --yahs` the pipeline doesn't reach scaffolding associated steps (_eg_ `process yahs_faidx` and `process hicstuff`) because the value `params.scaffold = false` …
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Hi,
After scaffolding, I followed the recommendation, executed the juicebox.sh, and used the out_JBAT.hic and out_JBAT.assembly to obtain a modified assembly in juicebox.
However, when I ran the jui…
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Hi!
I have been using grenepipe v0.12.2 for calling variants in 93 samples, and I had instances where merging paired bams step for one sample failed somehow in the middle of the run and everything…
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Hi, I want to use yahs to scaffolding my genome. I aligned HiC reads with chromap and scaffolded with yahs. Here is my scripts:
samtools faidx hifiasm.fa
chromap -i -r hifiasm.fa -o hifiasm.fa.in…
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Hi all,
Thanks for all the tools and support over the years.
I recently installed Verkko 2.2 with conda.
I am trying to get it to run in both --grid and --local modes on a SLURM cluster.
S…
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Assembly
- Manually curate the YAHS assembly
- Compare with GreenHill, classify Y chromosome contigs
Metrics
- New assembly metrics in the manuscript, comparing all kinds of new different …
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Hello,
I have some questions regarding treeval that I don't quite understand.
I recently assembled a genome, but the Hi-C results weren't very ideal. My advisor sent me a paper about gEVAL (https…