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I tried to run following given command:
`bash $path_of_the_pipeline/1Genome_construct_Pangenome.sh ref.fa query.fa > job.sh && bash job.sh
`
But 1Genome_construct_Pangenome.sh script is not provi…
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"We mapped reads to the pangenome to efficiently capture telomere length across the diverse
population. A references file of 500kb of subtelomere sequences was assembled from each of the
genomes (…
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Hello vg team
It is amazing the work you are doing.
I am relatively new to using vg and I would appreciate a little help with my question please.
I want to download an already constructed human pa…
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calc-hash-presence.py from [pangenome-hash-cor](https://github.com/ctb/2024-pangenome-hash-corr), does not yet allow me to compare protein sketches instead of nucleotide sketches.
I'd like to comp…
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- [ ] Check if the KBase model was using the correct genome
- [ ] Check if RAST annotation in KBase is redoing gene calls
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I ran PIRATE with 322 genomes (gff files) as input, but the file indicates 321 genomes. Is there any way to investigate why the count decreased from 322 to 321? The confirmation details are as follow…
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Hi,
I am experiencing the following error:
ValueError: The region is already with a different spot. A region belongs to only one spot.
version of PPanGGOLiN tested: 2.0.4 and 2.0.5
Steps to re…
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Dear sir,
Using Anchorwave-cactus, we have successfully constructed a graph-based pangenome from 97 samples. However, the centromeric region is proving to be quite confusing and is impeding t…
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In the Michelle's database table- there are a lot more rows than there are unique reactions (e.g. each different alternative enzyme or subunit gets their own row), so there may be a lot more red (wher…
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Thank you for developing such a great program! I've been using ppanggolin msa and it's been helpful. Here is the command I've been working with:
ppanggolin msa -p Pangenome_graph/pangenome.h5 --p…