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Hi,
I have been using FSA to align about 20 de-novo-assembled genomes that are about 1MB long. They are from different individuals in the same species. FSA runs, but it takes tons of memory, and …
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**1. What were you trying to do?**
I want to build GCSA index for a VG file generated from the Minigraph-Cactus Pangenome Pipeline. Because I met a "Size limit exceeded" problem in "vg index" run…
Sunhh updated
2 years ago
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**Problem:** SARS-CoV2 genomes already downloaded have ambiguity codes in them. Our pipeline needs to handle this in some way.
**Simon Heumos:**
Sequences like 'Y' or 'K' are encoding a nucleotid…
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I use vg (v1.39.0) construct on a vcf file (VCFv4.2) and hg19 but got the following warning: `"warning:[vg::Constructor] Unsupported variant allele ; Skipping variant(s)"`.
After some simple debug…
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Hi vgteam :)
@superjox @trgibbons
1. What you were trying to do:
I tried to use https://github.com/vgteam/sequenceTubeMap in order to browse certain positions `S288C_chrVII:95084-95584` of a yeas…
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Hello!
I am trying to visualize a pangenome graph I generated using the HPRC pipeline. In the last step of the pipeline (cactus-minigraph-join) I included the --viz flag to output pangenome plots f…
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Hi Erik,
I am doing some precision/recall analysis on a simulated set of 13 samples where each "sample" is a random mutant of a real-life plant chromosome. I introduced exactly 200 SVs per sample an…
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![upsetr](https://github.com/user-attachments/assets/d279210e-4f0d-47ed-9be5-56a190de255d)
Sorry for this question, but could someone help me understand this graph?
P.S.: IDs with "_REF" are ref…
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Hi @AndreaGuarracino and @ekg ,
Many thanks for developing "odgi"!!
I needed suggestions on the following problem, and if you could provide some answers, that would be super helpful.
1. I am int…
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Hi,
I used the Python API of ODGI to do the graph manipulation and used divide_handle() to split the specific node in the graph. I can successfully get the new handle when input is one offset, suc…