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Dear Guillaume Bourque's group,
Firstly, I would like to express my sincere gratitude for your remarkable software. It is indeed a significant contribution to the field. I've been using your pipeli…
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Dear BubbleGun team,
I believe that there is a bug in the “BubbleGun bchains” command when the option “--fasta” is used.
Bellow, I illustrate this potential bug with a specific example, using t…
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Hello,
> [!NOTE]\
> All comparisons I made here are on the chr21, between the PGGB graph and the .full MGC one build with GRCh38 as reference.
I was wondering about the completeness of the MGC …
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Hi I am trying to run pggb.
I make a fasta with 7 chromosomes i want to compare of 7 species. I names using PanSN
I run with the basic comand
./pggb -i test.fa -o out
I have not ouput
Also I t…
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Hi Pio,
Could you supply a small set of test files created by vg for pantera?
I get an error when using the GFA format created by vg as input.
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Hi,
This is a very cool tool, so thank you very much. I have so far made a "dual assembly" (http://lh3.github.io/2021/10/10/introducing-dual-assembly) with Nanopore reads and have made input files…
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Hi Jana,
I was in the process of indexing a cactus-pangenome based variant callset (seven diploids). The variants were filtered with vcfbub. I tested pangenie by running it with data on a single ch…
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Greetings, and thanks for this work.
The chromosome graphs for minigraph-cactus are available both in `.vg` and `.og` format, but as far as I know, only the `.og` version is the full, non-clipped, …
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Dear BubbleGun team,
I have used your algorithm to determine the number of bubbles and superbubbles in a pangenome graph of a LAB bacteria (the first approach mentioned bellow) and the classic algo…
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What can be the trigger of the following AssertionError in `edge2kmer()`? It is caused by specific scaffolds in one out of 14 assemblies (I identified one such scaffold by binary search but there are …