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Hi.
I'm creating a pan-genome graph of thousands of bacterial genomes using command : `cactus-pangenome ./1668-js-9 ./seqfile.txt --outName KP --outDir 1668-kp-9 --reference GN202435 --giraffe --vc…
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app installed with conda on ubuntu server
I then defined GETORG_PATH and ran `get_organelle_config.py --add embplant_pt,embplant_mt` with success
Hi,
I want to obtain the 4 possible circular p…
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Hi, Oushujun!
I have some animal genomes and want to annotate them by panEDTA. But now, I am confused about the some pipeline of panEDTA.
I read some others' issues about panEDTA, and they seem tha…
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Hi, I have managed to run `cactus-pangenome` for 31 _Arabidopsis_ genomes (using a Singularity image as pulled via `singularity pull docker://quay.io/comparative-genomics-toolkit/cactus:v2.7.1-gpu`). …
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I am wondering this to better understand how the layout algorithm works. In linear mode, the graph would be stretched longer, I would assume? Would it also make it more human readable?
By default in…
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Dear developer:
We are using livestock for pan-genome analysis, and we find that the genotyping-pipelines (https://github.com/eblerjana/genotyping-pipelines/tree/main/prepare-vcf-MC), although used f…
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Hello,
I just test pggb on a simulated data. I simulated a reference file(.fasta), the length of this reference is 3941bp. Then I simulated a query file(.fasta),the length of this query is 600bp. Th…
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Does this support GFA with genomes represented as Path records (as in vg and pggb)?
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Dear developer:
We were building a graph pan-genome using MC, we used "Create PanGenie-ready VCF from Minigraph-Cactus VCF" workflow, but we found that it was not feasible as soon as possible without…
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Hi!
I used PGGB to build a pangenome graphs of 15 assemblies. The PGGB pipeline splits the assemblies in communities, resulting in several GFA output for each communities. I would like to use odgi …