The format is based on Keep a Changelog and this project adheres to Semantic Versioning.
Initial release of genomic-medicine-sweden/metaval, created with the nf-core template.
- Extract taxIDs of viruses
- Extract Kraken2 reads with KrakenTools
- Extract Centrifuge reads
- Extract DIAMOND reads
- Screen pathogens:
- Map reads to the pathogen genome database using Bowtie2 for short reads and Minimap2 for long reads
- Call consensus sequences for reads mapped to the pathogen genomes