-
Hello, I downloaded the MERS genome from https://www.ncbi.nlm.nih.gov/datasets/coronavirus/genomes/. Given the fasta file, how do I build the panviral genome? Would my parameters be different? Ideally…
-
## Is your feature request related to a problem? Please describe
:warning: The pipeline is still work in progress, so documentation is really sparse.
## Describe the solution you'd l…
-
Hi,
I am trying to 2D lay a graph generated with minigraph.
I converted rGFA to GFAv1, this adds P lines for the reference and non-reference paths.
However, it seems that only the reference path …
-
Hi, I'm a Cornell ECE Ph.D. student participating on collaboration project with Erik. As far as I know, `odgi layout` is the most time-consuming step among all the tools provided in `odgi`. I tried th…
-
# nf-core/pangenome feature request
Hi there!
## Describe the solution you'd like
Evaluation of pangenome graph construction tools via mapping rate:
- Short reads: `giraffe` https://github…
-
ImportError: Bio.Alphabet has been removed from Biopython. In many cases, the alphabet can simply be ignored and removed from scripts. In a few cases, you may need to specify the ``molecule_type`` as …
-
**1. What were you trying to do?**
Try to identify variants by vg deconstruct with gfa file produced by PGGB
**2. What did you want to happen?**
I would like to get a vcf file from vg deconst…
-
Dear @npch @prenderj @RenzoTale88 @prasundutta87
Your code shows us a clear way to constrcut a pangenome. When I came to detect non-reference sequence, I can't find a help documentation. I don't und…
-
Hi all,
When having a large of genomes, in my mind, compromises should be made to achieve efficient computational and performance, such as removing the small variants emboded in the graph genome. H…
-
Hi I've been following this tutorial to evaluate VCF from PGGB: https://pggb.readthedocs.io/en/latest/rst/tutorials/small_variants_evaluation.html#
I get an error at the ```rtg vcfeval``` step, com…