(Posting my LessWrong comment here)
>If you’re paying $8k per billion reads
>This will likely go down: Illumina has recently released the more cost effective NovaSeq X, and as Illumina’s patents expire there are various cheaper competitors.
Indeed it did go down. Recently I paid $13,000 for 10 billion reads (NovaSeq X, Broad Institute; this was for my meiosis project). So sequencing costs can be much lower than $8K/billion.
Illumina is planning to start offering a 25 billion read flowcell for the NovaSeq X in October; I don’t know how much this will cost but I’d guess around $20,000.
ALSO: if you’re trying to detect truly novel viruses, using a Kraken database made from existing viral sequences is not going to work! However, many important threats are variants of existing viruses, so those could be detected (although possibly with lower efficiency).
This was per 10 billion pairs (so 6x cheaper). The specifications are here: https://www.illumina.com/systems/sequencing-platforms/novaseq-x-plus/specifications.html