Actually Ben's longest contig was only 29802 bases long, so it was 101 bases shorter than the third version of Wuhan-Hu-1 at Genbank, and it had one extra base at the beginning and it was missing the last 102 bases. I got the same result when I tried to use MEGAHIT without Trimmomatic, but when I added Trimmomatic to my pipeline, my longest contiguous sequence now missed only the last 30 bases of Wuhan-Hu-1: https://usmortality.substack.com/p/sars-cov-2-genome-assembly/comment/13659949. I probably used the wrong parameters with Trimmomatic though, or my pipeline is still missing other parts.