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Add BUSCO completeness to any assembled genomes.
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This is a thread to discuss how to build genome graphs with haplotypes that preserve the privacy of the genomes that the graphs were built from.
As a test data set, I downloaded a piece of chr20 fo…
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Dear curators,
I tried to dig deeper into the nature research paper ([Bradley et al., 2015](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4703848/)). In terms of mixed infection read analysis, the a…
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Just an issue to collect any relevant papers. For example, there's a whole Genome Biology issue on graph genomes at
https://www.biomedcentral.com/collections/graphgenomes (also see "Pangenome Graph…
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The Nature paper says that by using the software graph_peak_caller, we can do ChiP-Seq analysis on genome graphs. However, the original graph_peaker_caller paper says "Graph Peak Caller was developed …
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Hello, I'm a graduated student studying bioinformatics in South Korea.
I'm trying to do detect extrachromosomal DNA (ecDNA) in nanopore long-read targeted sequencing data.
I followed the workflow …
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I'm trying to train your model on the VG Dataset to reproduce the results. But I could not find the source for these files : VG-SGG-train.h5、VG-SGG-test.h5、VG-SGG-val.h5 in [lavis/configs/datasets/vg/…
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Hello there,
I hope all is going well on your side, and that you are having a wonderful day!
I just built a docker image for HLA-LA. For anyone interested, the Dockerfile is located here:
https…
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I'm thinking of doing the command line for this snakemake app differently; right now I'm not using config files much, just the sample name. How does the below sound?
each command would be successiv…
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Hi
I've been running Cactus on 3 different Barley genomes (planning to scale up to more genomes later). I've been running each job to create alignments of each chromosome from 1 to 7. I'm breaking …