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This is a request for a new feature rule to use PPanGGOLiN to create pagenome graphs for the genome projects.
I think we should use the Roary-defined Gene Famillies as input to `ppanggolin`. This w…
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+ [Application of a Novel “Pan-Genome”-Based Strategy for Assigning RNAseq Transcript Reads to Staphylococcus aureus Strains](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0145861)…
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## Motivation
Pangenomes are key to understanding the distribution of gene content and synteny across closely related genomes. Currently, the driving force behind this strategy is sequence alignmen…
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### Description of feature
Dear nf-core & pangenome team,
I have a few questions about your great program.
Based on the link (https://github.com/nf-core/pangenome/blob/1.0.0/modules/nf-core/w…
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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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Hi,
My name is Maggs. I'm working on a pangenome currently using the one-shot cactus-pangenome tool. After running for 7 days it produced *.sv.gfa.gz *.gfa.fa.gz & .paf.unfiltered.gz. However, it's…
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Hi!
Thank you for this amazing tool! I'm really impressed at how fast it complete the task :) I built a pangenome with 150 Vibrio parahaemolyticus isolates, but was confused about interpreting diff…
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Dear Panacus,
Thank you for developing such a great program.
I’m interested in testing the "Ordered Pangenome Growth Statistics" for a PGGB GFA file. However, the manual only provides guidance f…
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Hello,
I wanted to look at protein presence-absence of a broader group of genomes (several different orders from alpha-proteobacteria). Would you say it's possible with panX, or should I just run …
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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…