-
it would be nice to be able to decontaminate GTDB itself, but one of the problems we face there is that charcoal doesn't work well in situations where we have the exact genome in question in the refer…
-
## Environment
- [ ] Installed via pip (include the output of `pip list`)
- [0] Using a conda environment (include the output of `conda list && conda list --revisions`)
- [ ] Using a Docker con…
-
## Expected Behavior
map queries to GTDB then get taxonomy lca of best hits
## Current Behavior
-all taxonomy results are "unclassified" when mapping to GTDB
-the gtdb_mapping file has only a si…
-
I'm using the GTDB with kraken2 and get a .txt & .report file out, but I don't understand how to convert the GTDB ID of the .txt file to NCBI ID? There are several tools to convert between GTDB & NCBI…
-
### Checklist
- [X] There are [no similar issues or pull requests](https://github.com/micom-dev/micom/issues) for this yet.
- [X] The request is *not* specific for MICOM Qiime 2 plugin (q2-micom)
…
-
Dear @lskatz and @hcdenbakker
I am trying to download the GTDB database and building it using Kraken2.
When I use the following code as mentioned on Github-
`perl scripts/gtdbToTaxonomy.pl --…
-
I am trying to use a tool (Kraken2) using a specific rule (classify_gtdb). This rule requires a substantial amount of memory (at least 132 GB) for loading a database into RAM. However, I have encounte…
-
@dn-ra was thinking about `GTDB` compatibility of the classification results.
-
Hi,
I'm having the aforementioned issue. Here's the output I'm getting from `gtdb_to_ncbi_majority_vote.py`, including the parameters I used:
```
gtdb_to_ncbi_majority_vote.py v0.2.0: Translate…
-
This example uses the metagenome signature prepared in https://github.com/sourmash-bio/sourmash-examples/issues/12.
You'll also need to download the GTDB database as in https://github.com/sourm…