Looking at dotplots for PacBio assembly's alignment to the canonical reference
Larger image
Suppress warnings
Suppress warnings
Added show-coords command and output
Remove the '|quiver' from the contig names, as this screws up the kable formatting
Remove the LEN_1 and LEN_2 columns
Reorder columns
Readded the COV_Q column, since I understand it now.
Fixed a typo that was causing the requested COV_Q value not to show up.
Added sequences for all 60 var genes in 3D7
Added table showing var gene alignments to the assembly
Added section headings
Fixed typo
Fixed another typo