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Hi,
I have built the Graph Pan-genome, how should I use the tool to characterize it and dig deeper into the potential information it contains. Or is there any other analysis tool recommended.
Best…
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## Short description of the problem
I created a genomes storage consisting of ~2k genomes, and when I tried to run `anvi-pan-genome`, it exceeds my disk quota on the cluster and the job fails. It c…
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Dear developer:
We are currently using MC to build the pan-genome with very good results, and now we want to extract non-reference sequences for subsequent analysis, I would like to ask what is the e…
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I am performing roary pangenome analysis on hp genomes and I got several annotations for the same gene in the individual genomes. For instance vacA which typically has a single copy in all genomes has…
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I am running a pan-genome analysis using several Prokka annotated genomes and comparing them to complete genomes in the RefSeq database. The analysis works perfectly, however, in the output file the g…
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## Need
### TMB calculation today in BALSAMIC
The current definition is based on:
1. TMB was defined as the number of somatic, coding, base substitution, and indel mutations per megabase of genome …
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Hi,
I have used PanX successfully a few month ago. Now that i have migrated on ubuntu 18.04, i tried to reinstall it via git clone then conda install, but i failed to run the test... Here is the erro…
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Hi,
I am facing an issue regarding the reference path that pandora uses for genotyping the variants. It is basically using the less frequent supported path instead of most frequent supported path a…
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Hi Roth,
Thanks for your nice presentation last week on Pangenome analysis. I am wondering how CDHIT performs when there are a lot of genomes to compare. As you might know, uclust (embedded in usear…
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Nice pipeline,
Wanted to ask, does the pipeline implement nucmer at the start or the user should do that?
(lets say for a 5 genome comparison)
Thanks