Lupin-pathogensMultiple projects including various environmental DNA analyses, mapping sequencing reads and mitochondrial genome assembly of an ancient sample, whole genome assembly of a snake (black mamba). Setting up and testing software that our lab needs for the research
Principal investigatorMahsa Mousaviderazmahalleh firstname.lastname@example.org
Area of scienceBioinformatics
Applications usedMitoZ, BWA, eDNAFlow, general Command line, various containers
Bioinformatics projects and the underlying software they require are usually very memory intensive and running on local machines are not really an option. Also the input and output files are very large which is another hurdle in running the analyses on a local machine.
I’ve been testing different packages before employing them on Zeus/Magnus. In some cases I continued running the job on Nimbus if the software could do the job on a timely manner on Nimbus, for example in case of mapping reads to reference genomes using BWA.
Nimbus provided a magnificent opportunity for testing software before taking them to HPC and also allowed me to save time running analyses that could be finished successfully on cloud rather than waiting in Magnus/Zeus queues.