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Hi Linxing:
Thank you for developing this nice tool! I am curious about what's the functions does COBRA have in the classic virome pipeline as it's a new software.
For example, I used MEGAHIT to get…
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We have plans to replace the HV DB generated here with a curated internal-only reference DB, but there are still important improvements we can make to the public pipeline that will significantly impro…
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https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0223364
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Hi!
First of all, thank you for putting together such a nice pipeline! It's very convenient to have all of these tools in one place.
I installed BEAV using conda as per instruction on the readme…
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beav --input shivanshi_bakta_annotation/Plant_Pathogen/Pectobacterium_carotovorum/Pectobacterium_carotovorum.fna --output beav23/ --skip_tiger --bakta_arguments '--db $HOME/Shivanshi/shivanshi_bakta_…
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I installed using mamba. When I run, I get the following error concerning module 'skip'. I checked and it's installed and Python finds it just fine. Any idea as to what to try?
[2022-09-29 14:16 IN…
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Hi all,
Thank you for an amazing tool!
I use this tool a lot (viral metagenomics data) and I have noticed that the predicted proteins are translated with different genetic codes:
For instance,…
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Hi!
Thanks a lot for developing this useful tool! I am currently trying to run it on a set of ~2,000 viral genomes.
I followed the GitHub instructions and:
- I also added prodigal to the path (…
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* pharokka version: 1.7.2
* python version: I use mamba to run commands? But my mamba version is 1.2.0
* Operating System: MAC
### Description
Hello, I am trying to detect phages in .fna (FAST…
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Hi @guipenedo , I used your substring dedup script to perform deduplication on a dump of cc and did some manual inspection. I find that some resulting duplicates a bit strange.
For example,
```
…