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Hi
I tried to scaffold my contig level genome with my hic data but failed with the segmentation fault error.
I think this error can be occurred due to the large hic alignment, which is about 700Gb…
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Hi,
Thank you for creating and maintaining YaHS. I installed YaHS 1.2a.1 by `mamba install yahs -c bioconda`.
~100x Hi-C data was mapped to assembly after purge_dups by Chromap following the pip…
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Hi, Haowen
Chromap is super fast when I use pair format. But I want to use chromap for assembly scaffolding pipeline (chromap + yahs), espeically for large plant genome. Since yahs accept the bam o…
baozg updated
2 years ago
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Hi Yoshi,
`contigs.omnic.dedup.sorted.bam` file required as input of the YaHS workflow is currently not symlinked automatically by the pipeline. This could be fixed by symlink from e.g. salsa run out…
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For three different assemblies, the output from YAHS is exactly the same as the input assembly. I used the Arima-HiC Mapping Pipeline to map my HiC reads to my assemblies. Assemblies are either HiFi-o…
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Hi Zhou:
After running yahs, I have gotten worse assembly metrics than with the hifiasm-only assembly. The number of genome scaffolds has increased from 1,200 to 9,500, the scaffold N50s have decreas…
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Hi
I am trying to scaffold the genome of a plant species with YAHS. However I am getting an error that I can't seem to find a work around it. Here is the log file, any suggestions on how I can make…
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Hello,
Hello and thanks for creating yahs!
I'm running the following line in order to generate the alignments file using juicer pre and it seems to run fine but the .txt file is empty.
(yahs/ju…
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I tried many yahs versions and they all reported the following error. Hope to fix it.The following is the content of the error report.
[I::dump_links_from_bam_file] 434 million records processed, 727…
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Hi,
thank you very much for this nice tool, it does a great job of scaffolding our ONT-generated assembly using HiC reads.
However, after scaffolding by yahs, gaps of a standard 200 bp length a…