-
Hello,
Recently I have run into an issue with odgi inject when trying to inject genes and exons as paths in a graph. When running odgi inject using a bed file with overlapping coordinates (for inst…
-
Hello,
**Context**
I have built a pangenome graph using VG, converted it into ODGI.
Now i want to have an overview of its complexity and remove the problematic regions. In order to do so, I foll…
-
**1. What were you trying to do?**
Running vg autoindex on yeast assembly together with known variants from ensembl:
```
vg autoindex -t 2 --workflow giraffe -r resources/genome.dna.saccharomyc…
-
Hi,
I'm trying to run pggb on a set of five assemblies of an insect genome. The mash distances (`-32 -s 10000`) ranges between 0.004 to 0.009, and the genome size is ~230Mb.
I've ran a test using th…
-
Hi there,
I generated a graph for five human individuals with the following command:
```
pggb -i /g100_scratch/userexternal/mungaro0/pangenomes/pangenome_ref_guided_pggb-v4.fa.gz -o /g100_scratch…
-
I used pggb for graph-based pangenome.
Some regions are disappearing from the alignment.
pggb -p 90 -s 100000 -n 18 -k 311 -o ${name}_90_10w -t 50 -T 40 -U -v -L -m -V FB19_011_3_pseudomolecules…
-
Hi,
What does the long range link mean? I saw some very long range links connecting the two ends of the chromosome, how should we interpret these links? If those links are caused by repeats, how ca…
-
Using the Dockerfile from https://github.com/pangenome/pggb/pull/231 I get quite an ugly DRB1-3123 graph:
![DRB1-3123 fa gz b1e1a2d 417fcdf a8de103 smooth final og lay draw_multiqc](https://user-im…
-
Hi,
With the [prebuilt GRCh38 pangenome graph](https://zenodo.org/record/6499594) I am getting an assertion error.
`minigraph -t 1 -cx lr GRCh38-90c.r518.gfa.gz reads.fa`
`minigraph: gchain1.…
-
If I'm building a graph of n genomes of E.coli, is there an option in pandora to get the vcf of these genomes?