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- [ ] look at Leinweber K (2018) TIBHannover/BacDiveR: a programmatic interface for the Bacterial Diversity Metadatabase. [Zenodo.](doi.org/10.5281/zenodo.1308060)
- [ ] Decide whether the package sh…
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From Elissa: [In the Phenome Database], you can see some potential mapping, e.g. measurement 1501 has "altered susceptibility to bacterial infection" phenotype (MP) and "response to bacterial infectio…
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Hi,
I have just started using Kraken2 for a classification of metagenome reads into fungi. A previous read mapping to RefSeq (about 500 species) only identified aobut five OTUs. Kraken2 identified …
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Hi guys! First of all thank you for doing this work. I think compiling and curating these databasets is really useful and would have been difficult. I have used this databases to do taxonomy assignat…
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### Description of feature
Also recommended by Prokka developer! nf-core module already exists
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Hi there,
I wonder what parameter i should set (eg negative_taxids ?) when i am performing blastp against protein databases, if i would like to filter out all prokaryotic blasting results, as i am …
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Hello everyone,
I was trying to build Krake2 databases with GTDB. However, since GTDB consists of only bacterial and archaeal sequences it would be ideal to build it along with the viral Refseq. Im n…
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Hi Diener,
would it possible to provide detailed description on the procedures that generated those GEM reference database? I found it quite useful while I am hesitating to use it in my manuscript wi…
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Hi Paul,
I have run framefix on a few bacterial hybrid assemblies (ONT+Illumina) generated with Unicycler or Flye/Racon/Pilon. I am using the Uniref90 database:
/path/to/framefix /path/to/assem…
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### Operating System
macOS
### Other Linux
_No response_
### Workflow Version
v1.2.0
### Workflow Execution
EPI2ME Desktop application
### EPI2ME Version
v5.1.14
### CLI command run
_No res…