This release adds base alignment to minigraph. It represents the first major improvement to minigraph. Specifically, this release attempts to connect linear chains with the graph wavefront alignemnt algorithm (GWFA) and produces the final alignment with miniwfa under the 2-piece gap penalty. Graph generation also considers base alignment. This gives more accurate graph alignment and generally simpler graph topology. Note that minigraph still focuses on structural variations and does not generate base-level graphs. To endusers, minigraph remains similar feature wise.

Notable changes:

• New feature: option -c for base alignment and graph generation. In the alignment mode, the option adds the cg:Z CIGAR tag like minimap2. Graph generation still works without -c but applying this option is generally recommended now.

It should be noted that the base alignment is currently slow for species of high diversity. This will be addressed in the next couple of releases.

(29 April 2022, r524)