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Hi,
We would like to use this dataflow and it would be great if we could know what type of machine you used (especially nproc and memory) and how long it took to run the dataflow. We'll spec our VM…
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Hello,
cool package, thank you. :-)
Is there a possibility to download all genomes that belong to a certain genus or family? The way I see it, I cannot use the taxid of the genus or family as t…
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Hi,
Thanks for the gtdb-taxdump. I´m working on Silva , is there any available tax dump ?
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I'm trying to use a clustered version of the NR database for taxonomy assignment but am running into some issues. Any assistance would be appreciated.
## Expected Behavior
When running `mmseqs cre…
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Hi there,
I am trying to update the GTDB -r207 database I have downloaded using Struo2 with my own MAGs. It is not clear how I get some of the information including "ncbi_organism_name", "gtdb_taxi…
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I'm trying to parse the GTDB r207 taxdump with [`taxopy`](https://github.com/apcamargo/taxopy) and I got the following error:
```python
taxdb = taxopy.TaxDb(taxdb_dir="gtdb-taxdump/R207")
```
``…
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Dear Shenwei,
Thank you very much for providing a good tool, I am trying to adjust the output table as desired according to KMCP format.
- Currently I use search with all the databases you provide…
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When you create a taxdump using `create-taxdump` (ICTV taxonomy, for example), the taxids "skip" some numbers. For example:
```
$ head ictv-taxdump/names.dmp
1 | root | | scientific name |
2872…
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Hello,
I would like to run Hecatomb only using the assembly or ctg_annotations module, but I end up with an error.
Here is an example code:
hecatomb run --reads /reads ctg_annotations --threa…
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I've been taking a deep dive into eukaryotic metagenomics and EukCC seems like a great tool to have in the repertoire. From the documentation, it seems that EukCC version 2 is still in development so …