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- [ ] Literature review on Vibrio Pathogenicity Islands- Vanessa, Brian and Latifah.
- [ ] Work out the relationship between VPI and CTX phage- Vanessa, Brian and Latifah.
- [x] Get 10 cholera seque…
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Hello Prokka team,
I have been using Prokka with a default setting for annotating E. coli genomes. I noticed that the identified virulence factor genes are different between ABRicate (VFDB) and Prok…
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Hi,
We have tried the VirulenceFinder database, but when we look at the output files the naming of the virulence genes seems to relate to "cluster numbers". Looking at individual files it seems like …
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Hi,
I have tried P-DOR over a batch of 347 FASTA samples. It went all smooth, till the end were I faced this error:
Date and Time: Wed Sep 18 15:06:05 2024
Possible outbreak detected!
Gen…
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1. (How handle genes that are intrinsic to a species)
2. What tool(s) to run - any reason not to replicate Grace's approach from https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.…
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Hi, Torsten,
I am using the abricate to screen all the virulence genes from my data. One purpose is to extract all the virulence reference sequences in the database which are in my sequencing data. M…
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Review existing tools in the pipeline if they can take in Nanopore data. If not, find a suitable alternative for long reads.
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PHI-base currently has an evidence code 'gene deletion:cluster'.
**Example 1**
There is only 1 PHI-base entry using this evidence code! PMID:28288207
http://www.phi-base.org/searchFacet.htm?quer…
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I have tested IslandPath-DIMOB to search genomic islands associated with
E.coli virulence genes and get the final results with start and end
position of each GI. I just wonder how could I get the d…
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When I try to run abricate against my bacterial genomes .fna (total 20 in number) using the VFDB database, the result shows that there are no genes in any of them.
Command used: abricate --fofn lis…