# Hackathon November 2020 --- <!-- Put the link to this slide here so people can follow --> slides: https://hackmd.io/@Hackathon-November-2020/HJzJqzyqD --- # Project 7: Bacterial DNA analysis pipeline --- ## Primary focus Public health project after extracting DNA from bacterial samples and running MinION and ILlumina extraction, how to constrcut the entire pipeline for genomic analysis to phylogenetic analysis and detailed analysis of the core genome. --- ## People involved ### Proposed by - Joana Moreira da Silva (CIISA) ## Group members - Joana Moreira da Silva (CIISA) - Akshatha Nayak - Ahmed Madgy Mustafa --- ## Progress so far - we will try to construct the pipeline on the premises that we have a sequence which is ready to use after WGS analysis and all that work needed to get those sequences ready to use (Project 2) - searched for the command lines of the softwares will need - Resfinder, PlasmidFinder. Others may be added after succesfully impleting these - decision to implement pipeline locally due to disk consctrition --- ## What to do next? - install the sofwares locally on a Conda environment ( we have already found the scripts on github and bitbucket) - using available sequences on NCBI, check if the softwares were installed correctly and from there, do the first part of the pipeline - Resfinder + PlasmidFinder --- ## Second Day - decided to use a container found for ResFinder - Some problems with it: - the latest tag wasn't working - even after finding a working tag, it still gave an error (wasn't pulling the image) - with the help of Luca, we succedfully pulled the docker - it appears some sort of database is missing, which renders it impossible to work ( or so we think) --- ## What to do next? - ...