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Hello,
I'm trying to generate a new taxonomic tree (described on Generating the taxonomic tree and genome vitals references) to use with gottcha using a specific set of viral genomes.
I generated a .…
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![Image](https://user-images.githubusercontent.com/1882209/191572992-2639528d-c98e-4f5c-b404-e2f70b3854f2.png)
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I've been running vRhyme on some of my test data [SRR11140750-test.zip](https://github.com/AnantharamanLab/vRhyme/files/13515750/SRR11140750-test.zip) and vRhyme doesn't generate any output bins (alon…
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Thank you for this wonderful tool!
Should we filter out the host (human) genome before executing the pipeline e.g. using kneadData or fastp? the same also applies to the PhiX genomes?
I tried He…
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Hi,
I want to map my reads to a merged genome (virus/host/mitochondria). I noticed that it's better to provide the gtf/gff file when building indices.
I was wondering how can I generate merged …
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Hi, a big thank you to the developers of this useful and versatile tool. I am using sourmash to detect and remove undesired prokaryotes from WGS datasets in my de-novo assembly pipeline of prokaryotic…
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Hello,
I am currently struggling with metagenomes obtained from environmental biofilms (river rocks). I have 50 metagenomes but I obtain only 100 checkV high-quality viruses. I would expect a lot m…
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- circular graph is not a problem, MongoDB deals with this and does not enter an infinite loop
- how specify "entry point" of the graph?
- how "backtravers"? *
* Here we really only need 2 links…
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Meta-issues for database-related experimental design discussions
- [x] How many genomes?
- [x] Which genomes to select?
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- **Organizational Page**: [Pathogens](https://github.com/NCEAS/open-science-codefest/wiki/Pathogens)
- Proposer: Bill Mills
- Field: Genomics (particularly WRT to pathogens)
- Computing: Python
- Lo…