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Not an issue with the program but looking for a bit of advice.
I'm building a BURST database based on refseq-microbial for use with SHOGUN. How did you build the example genome taxa file?
I'm gu…
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The setup files `rhimgCAMI2_setup.tar.gz` and the genomes `rhimgCAMI2_genomes.tar.gz` used for the _A. thaliana_ rhizosphere mock data have been downloaded.
- `wget -P /path/ https://frl.publisso.d…
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ideally there would be a script to generate test datasets from genome sequence data.
classic approach is to take reads from isolate genomes and mix them in known abundances.
need to get isolate genome…
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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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Potential environmental databases we could pull from. (Linked API page where I could)
- [MGnify (formerly EBI Metagenomics)](https://www.ebi.ac.uk/metagenomics/api/docs/#/)
- [MG-RAST (metagenomic…
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Building a microbial nt database
Dear staff,
I am trying to build a microbial-nt database. According to the tutorial I run the following command:
_krakenuniq-download --db DB --taxa "archae…
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**Tool Details**
- Name of tool: Roary
- Tool homepage: https://github.com/sanger-pathogens/Roary
- Tool description: Roary combines prokka output (annotated microbial genomes) from multiple org…
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If you have a lot of genomes, your project XML is going to be huge. If all the information is the same, we should be able to get the taxon ID from the data file or even the file name.
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We are work…
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[InStrain enables population genomic analysis from metagenomic data and rigorous detection of identical microbial strains](https://www.biorxiv.org/content/10.1101/2020.01.22.915579v1)
Coexisting mi…
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Dears, I am running the test with the file you provide. However, it seems there is an issue by calling blast.
```
./scripts/VITAP.sh assignment -i test.fasta -d ./DB_20240115_IMGVR_expanded -o test_…