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Hi,
Thanks for your user-friendly software!
I am looking for a way to extract a longest path in a GFA file.
But while I try
`gfatk linear xxx.gfa`
There is an error
`Error: Edge coverage not f…
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Hi,
I am trying to make a graphed pangenome by using cactus. When I use contig-level assemblies to run this pipeline, everything goes well. But when I scaffold these contig-level assemblies to chro…
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Thanks to vgteams for developing such a useful tool. I want to map nanopore reads to a pangenome graph ,which can do by vg map. Is it possible using giraffe to map nanopore reads by adjusting paramet…
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Hello,
I have been using pggb for a while now and over a couple of different builds. I have been able to run it previously and can still run a previous version (pulled February 8) without seeing thi…
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Hi @lh3, as per title - is minigraph suitable for generating bacterial pangenome graphs? All of the examples were eukaryotes that I just saw so just wondering how it will handle gene reassortment and …
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Hi, there are multiple missing images in the markdown files. The links are broken as they point to a local folder. Here are a few of them:
in https://github.com/YaoZhou89/TGG/blob/main/1.Genome_ass…
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Hi @glennhickey,
I've started `minigraph-CACTUS` without major problems on my HPC cluster. However, at step 3 (_cactus-align_) the script terminates with an error, and I'm unable to generate the **…
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Hello!
I want to extract red boxed region from the pangenome graph (image 1) and build a new graph. With odgi extract command, I can extract the region, but each sequence gets truncated and realig…
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Hi @ekg,
For some reasons, after trying to install `pggb` with this command **_conda install -c bioconda pggb_**, I'm presented with the following error code:
> (quality_check) 05:18:01 | mat@ne…
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Hi,
Recently, i want to map the short-sequencing reads to the graph genome using recently published `giraffe`. The first thing I need do is to generate a high-quality and no-reference bias graph ge…