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Hi, we recently downloaded the Pangenome assemblies in the AGC format, and we extracted individual assemblies in fasta format. We noticed that contig names do not match human chromosome names. Are we …
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Hi,
I have executed pyseer and I would like to map my unitigs not to the list of my input files but back to just one fasta/gff file that represents my pangenome.
This file contains representat…
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Hi,
I am experiencing very different results when using ppanggolin projection with gbff or fasta files for the same genome.
Steps to reproduce:
```
# get a bunch of genomes to create the pan…
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Hello,
I'm trying panTools for the first time to build a pangenome graph from 4 polished assemblies of ~70mb in size. I tried following the instructions, and the program starts, but then just sits t…
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Hi,
I am running the mc pangenome pipeline on SLURM. Among the `minigraph_map_one` jobs, a few of them have error like `FileNotFoundError: [Errno 2] No such file or directory: tmp/......./deferred`…
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Hello,
I have created a pangenome of the subset of my (mammalian) data with minigraph-cactus, but I have a larger amount of edges and nodes than I would expect. I have 1,743,464 nodes and 2,386,085…
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Hi all, I generated a pangenome with Minigraph-Cactus with this command:
```
cactus-pangenome 3_MC_all/js-3_MC_all ./scripts/3_MC_all.seqfile \
--outName 3_MC_all \
--outDir 3_MC_all \
--refer…
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Hi,
I want to align the short reads to graph using vg giraffe and get a bam file, but i got the following error report. The VCF and graph (GFA file) were constructed using [PGGB](https://github.com/…
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Hi,
I am using the following command to run Panaroo and getting a file extension error. I annotate the genome using prokka. Besides that, I tried using the off file from NCBI but still got the error.…
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Hi.
Now I have the `.gbz` graph file, and I want to simulate the third-generations `long reads` data from a pangenome graph. Can VG simulate the third-generations long reads? Or if there is some m…