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Hi folks
For k-SLAM installatin I need to download the NCBI taxonomy, bacterial, and viral genomes (i.e. using install_slam.sh). If I already have these downloaded somewhere can I just point to the…
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Hi, I have a dataset of 2905 genomes and would like to use Orthofinder to generate a phylogenetic tree. I used 72 cores and it has been 7 days and it is still running. Do you have an estimation of how…
ghost updated
2 years ago
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Hi,
Thanks for developing state-of-the-art technology for prophage detection.
I have a strange bacterial genomes which have a variety of mobile genetic element in their genome, so I want to custom…
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Hello,
I am trying to use Ptolemy extract (in addition to Panaroo for Bacterial Pangenome) but I have an error when I am running the following command on my gff3 file obtained with Bakta:
```
ja…
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* pharokka version: 1.7.3
* Python version: 3.10
* Operating System: Linux
### Description
I ran the command as below
`pharokka.py -i 5_redundant/${line} -o 6_pharokka/${sample} -t 1 -f -d /bee…
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I really would like to use your visualization tool with bacterial genomes, but all of the examples I can find are with human data. Can you please provide some examples of exactly how to format your da…
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Hi, I run this pipeline on my own phage genomes and bacterial genomes to predict interactions between them. Based on the output, it seems that only one bacterial host is predicted for each phage genom…
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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…
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Hi,
I am struggling to workout and estimate minimal resources to run cactus for 100 genomes mammal size.
I can use CPUs, GPUs but I need to estimate amount of resource for an amount of time (project…
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I noticed that a lot of memory is used when `link_clusters.pl` is run in parallel. Can you explain what would determine the memory usage for each execution of this script? Depending on the response, …