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### Test assembly:
[kleiner_2015.fasta.gz](https://github.com/EBI-Metagenomics/emg-virify-scripts/files/4414825/kleiner_2015.fasta.gz)
### Observation
It seems that VirSorter predicts a prophage…
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_From @ValWood on March 28, 2018 16:10_
human has 1403 annotations to "symbiont process". I find these very misleading.
The practice of annotating human genes to viral processes seems very stran…
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Do you need to create databases or is there a better option?
I created a database for copepods:
```
makeblastdb -in ../blastpacope/genomas_copepods/ncbi_dataset/data/db_all_copepods.fna -dbtype…
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Hello,
I am wondering whether or not VIBRANT trims any non-prophage sequences, such as phage contigs with DTRs on both ends (signifying a likely-complete viral genome, for example).
I'm thinking …
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After installing either the latest version from git or source version v0.42.3 from http://pachterlab.github.io/kallisto/download.html on my 32-bit Linux (Debian), index building crashes:
~/Software/k…
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From @lakras:
```
+ metagenomics.py kraken2_build /home/dnanexus/tmp.cz7tNSRcma --tax_db=/home/dnanexus/tmp.doXVmDiwl0 --standard_libraries nr --taxdump_out taxdump-kraken2x-ncbi-full-nr-20160923.ta…
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Remove unused packages from https://github.com/EBI-Metagenomics/emg-viral-pipeline/blob/master/cwl/requirements/conda_env.yml
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GO:0009405 pathogenesis
Has the comment: note that this term should not be used to annotate gene products that are involved in the host response to pathogenesis. It should only be used to annotate tho…
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Currently, we are using the default model for VirFinder predictions.
However, we are particularly interested in predicting also eukaryotic viruses (and not only phages) with VirFinder. I tested th…
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hello there!
Im sorry if this is a stupid question but I am trying to build a database comprising of both archaeal and bacterial sequences from GTDB and viral refseq sequences. I would also like to u…