vrubels
commented
4 years ago Minimap2 would be immensely useful for my work as well. Lately on larger assembly projects I've run into issues where blast is unable to find hits that truly exist in the assembly, which I think are due to excessive memory usage. In addition I find queries even on more reasonably sized assemblies can take far longer to run than equivalent queries run locally using minimap2 take. If I'm not mistaken minimap2 is the current gold standard for assembly mapping accuracy too.
Bandage has become a vital too for me and others to analyze Shasta assemblies. The Blast functionality is essential for that, but Blast is an old mapping tool and is slow and not particularly suited to map assemblies from long reads. A much better tool for that is minimap2. Any chance that you could add minimap2 support to Bandage, similarly to what you do for Blast?