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Dear odgi team,
I have used the BubbleGun algorithm recently published to determine the number of bubbles and superbubbles in a pangenome graph of a LAB bacteria.
The command I have used to calc…
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Hi
I have a whole chromosome graph from a pangenome alignment which includes paths along different genomes (20). I've embedded genes/exon/CDS into the graph based on a single path (the known and we…
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my code :
vg rna -p --threads 20 --transcripts /data/yxzhu/Oaks/Ref_genome/Ref_genome/Quercus_variabilis/Quercus_variabilis_onlychr_rename_converted.gff3 --use-hap-ref --gbz-format --write-gbwt Querc…
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Hi
Two features which I think would be really useful in sequenceTubeMap are:
1. On hover over a node or path more information is displayed i.e. all paths passing through the node and the sequenc…
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+ Metapangenomics of the oral microbiome provides insights into habitat adaptation and cultivar diversity
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-02200-2
https://doi.org/…
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Nice tool!!! I also have a similar idea for developing such a tool to genotype all genes witch cnv for large cohorts. The problem is you used HPRC etc. to construct a database, how can I construct a n…
yeeus updated
2 weeks ago
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I think this issue is related to something that has been mentioned previously here, but I'm not sure that it is resolved.
I am using GSalign to align and call variants from a series of assembled ge…
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Hello,
I want to know if I have some de novo genomes to build a graphical pangenome, except the recommended method [https://github.com/pangenome/pggb](url), whether the `minigraph` [https://gith…
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Hello, I am using Roary to generate a pan-genome with 682 .gff files obtained from Prokka.
The Roary command I'm using is python3 roary_plot.py --label mytree.newick the tree made by these command is…
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(panX) anna@Anna-PC:~/work/pan-genome-analysis$ sudo sh run-TestSet.sh
Traceback (most recent call last):
File "./panX.py", line 6, in
from pangenome_computation import pangenome
File "/h…