Thanks to Paul Oluniyi I can add some more details on method. viral-ngs v. 1.25 was used on DNAnexus. Quoting Paul:
“First, we demultiplexed individual libraries, removed reads mapping to the human genome or to other known technical contaminants (e.g., sequencing adapters), and filtered the remaining reads against all previously published SARS-CoV-2 genomes. We performed de novo assembly using Trinity software and scaffolded contigs against the reference SARS-CoV-2 genome from Wuhan (NCBI accession number: NC_045512.2).”