Meeting with BugSeq on June 4th, 2020
BugSeq
June 4th, 2020
Prenotes
What we plan to do:
Project 1: Deploy a lab-in-suitcase for genomic pathogen surveillance in Cebu: Project Charter
Project 2: Create an open playbook for deploying genomic surveillance: https://app.jogl.io/project/285
Kahlil's background: /kahlil/Kahlil Corazo, Open Playbook PM
Questions
(btw, I'm a bioinformatics noob)
My understanding of the standard Nanopore bioinformatics stack: Bioconda Snakemake medaka Pomoxis minimap2 Flye
Is BugSeq a replacement?
Is there training on analysis of output https://bugseq.com/demo/sars-cov-2 (part of the project is to recruit lab techs and train them)
Do you bioinformatics support be centralized? Per deployment? The lab techs themselves or dedicated bioinformaticians?
What is the input file? We have bandwidth issues in developing countries, the location of Project 1 and the target of Project 2.
Notes in Roam