Actionpoints.md

[LatifahBenta]

• [ ] 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 sequences from NCBI, Should be 4Mb, from Kenya or East Africa- Vanessa
• [x] Do Serotyping and Strain typing (MLST) on the sequences- Latifah
• [ ] Look for Biotyping and Strain typing tools- Brian
• [x] Run Abricate to determine AMR and Virulence genes- Brian
• [ ] Isolate CTX Phage genome from the V.cholerae genome- Vanessa
• [ ] Characterize the CTX Phage in terms of AMR and Virulence- Latifah
• [x] Install BEAST for phylogeny- Brian
• [ ] Phylogenetic tree- ParSNP- Latifah

[Natasha-Adongo]

I was not able to get African genomes because most of the ones available were from EBI-ENA and were only raw reads with one being around 4.5GB so Brian and talked and we will just use the ones from anywhere. The goal is to test out our hypothesis.

[LatifahBenta]

Done with Straintyping using PubMLST. I will update on github on the different strains.

[Brian-Kimutai]

Screening for AMR genes and Virulence genes is Done.