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hi,
this is not an issue. plz bear with me since i am new to this. in the example to construct, you use the ".vcf.gz" file. currently, i have the ".fna" file, but how or where do i get the correspo…
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One of the "problems" I'm having with metagenome graph-based differential abundance (implemented in #303) is that there are *a lot* of cDBG nodes, so even catlases built with R5 have *a lot* of domina…
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Hi,
Thanks for this awesome tool to enable graph file manipulation!
I wonder if there is an easy way to extract haplotypes based on specific traversal paths? I understand that odgi can extract …
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Hello!
I have obtained three graph pan-genomes through three software: Minigraph, Minigraph_cactus and Pggb, which contain 12 mammalian species. Then I also have nearly 500 next-generation sequencing…
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Hi @eblerjana,
I am running pangenie, using the HPRC-CHM13 (88 haplotypes) dataset VCF files, as you've specified [here](https://github.com/eblerjana/pangenie?tab=readme-ov-file#pangenie-v211).
…
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Dear vg team,
I read the recent HPRC publication 'A draft human pangenome reference'. Inspired by this paper, I tried to call SVs only belongs to sample A but absent from sample B. The general step…
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Hi,
I want to use your HGSVC graph for my own analysis. In your ftp website, I saw many different graphs. As following:
1) https://cgl.gi.ucsc.edu/data/giraffe/mapping/graphs/for-NA19240/hgsv…
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Hi,
I construct a colored dBG w/ Bifrost and remove the overlaps using gimbricate. From the documentation I read that seqwish can now be used to extract the paths of the constituting genomes throug…
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Hi, I ran pggb to build pangenomes for 10 bacterial genomes (Ecoli). The command is `pggb -i merged.fa.gz -o 10n95p -t 20 -p 95 -n 10 -S -m` and it can work well. But i have some confused with the par…
zwh82 updated
12 months ago
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There's not a lot of standalone tools for bubble popping, so thanks for implementing this one. It's an interesting problem, and I'm a big fan of standalone implementations of core assembly algorithms.…