Bash scripts used for analysis of SARS-Cov-2 sequences on Clinical Institute of Special Laboratory Diagnostics, Division of Pediatrics, University Medical Center Ljubljana.
To run analysis on Illumina data it is needed to activate conda enviroment with iVar https://github.com/andersen-lab/ivar
To run analysis on Nanopore data it is needed to activate artic-ncov2019 conda enviroment https://artic.network/ncov-2019/ncov2019-bioinformatics-sop.html