Migrate improved CoV assemblies to lovelywater, and annotate them

[taltman]

For the manuscript, we improved the assembly of all CoV/nido from novel taxa. But those improved assemblies have not made it over to lovelywater.

Example using AmexNV:
aws s3 cp s3://lovelywater/assembly/cov/SRR6788790.cov.fa .

This only has the "R contig".

Anton pointed out that the improved genomes are here:
https://serratus-public.s3.amazonaws.com/ak/epsy/epsy.tar.bz2

If you look in the right cluster, you can check out the contigs for SRR6788790:
`OTU-SRR8244388/Epsy$ egrep "^>" SRR6788790.epsy.fa

NODE_3_length_19124_cov_65.568632
NODE_11_length_12596_cov_95.354468`

For consistency with the manuscript, we should push these improved genomes to lovelywater. Also, this will require rerunning DARTH on these updated assemblies.