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Hi, thank you so much for the great tool!
When I run salsa with my contigs file and alignment bam file, this is what I see, and result in the same number of scaffolds as in the original contigs fil…
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Hi,
I am trying to use HapHiC to anchor a haplotype-collapsed genome (hifiasm p_ctg), and I found that HapHiC perform not so good, **especially contig ordering,**
HiC data was mapping following Hi…
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### Ask away!
Hello, thank you for developing this pipeline.
I was able to create a .hic file, but I want to use this to improve my genome assembly. I want to scaffold my assembly based on the con…
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Hi,
The commandline workflow posted in the other bug report has issues.
But note, it is rather simple and would be sufficient for most people.
It is much easier to get to work this than installin…
ahcm updated
10 months ago
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I would like to use the command line functionality of hicexplorer to automatically plot hic matrices as part of my workflow. I have generated `.hic` files that can be loaded by Juicebox for manual ed…
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Hi Yoshi,
YaHS is creating two folders output/ and output_for_curation/ but salsa and 3ddna not, so they seem to stop after not finding these output folders with messages.
```
Writing expected
W…
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Dear colleague,
I get an error in the pipeline during Juicer pre and perhaps related to juicer tools. I use conda in an ubuntu 22.04
This is the input
(hic-scaffolding) jpons@tesla:~/Downloads…
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Is there an option to run Yahs as a contig correction tool only?
After the initial assembly I want to first be able to break the contigs where needed before removing duplicates and running yahs for…
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Assembling Lampropholis with the best pipeline discovered with Bassiana/Tiliqua
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Run AutoHiC on bassiana YAHS and compare results