As part of the project, two main parts are assumed: biotechnology - related to the growing of bacterial strains and the implementation of a series of experiments using the Oxford Nanopore method to read DNA sequences; IT part - related to obtaining DNA sequences and performing specific data analyzes in order to identify those mutations of bacterial strains that have the potential for the greatest future applications.
To complete the data processing part of the project, it is necessary to install and become familiar with specific tools and environments. To this end, a team of IT specialists composed of A. Czmil, M. Ćmil, M. Wroński, D. Strzałka did a series of works that included: creating a container image with a runtime environment, and thus the necessary libraries and tools for processing sequential data. After downloading, the container is ready to start immediately. Container images have been added to the image register and script prototypes have been created to pipeline genomic data processing. To this end, it was also necessary to become familiar with the genome assembly process; testing a previously prepared server prototype on sample data from bacterial sequencing (data available from the Internet); tuning tool parameters. Tests were carried out on the genomic sequencing tools Poretools, Canu and Nanopolish.
Works were done reomotely.
