Severe acute respiratory syndrome coronavirus 2, GISAID ID: EPI_ISL_416411
ARTIC v1, library prep NexteraXT, sequenced 150 bp PE.  Using minimap2, short reads mapped to SARS-CoV-2 NCBI accession MN908947.3. Using samtools, proper_pairs (samflag 2) mapping to MN908947.3 retained, unmapped reads (samflag 4) discarded (to filter out non-SARS-CoV-2 cDNA).