Are there certain alignment methods/tools which perform better with a high density of indels? I have a set of experiments which should result in WGS reads with a high density of indels. 

Question: Are there certain alignment tools/methods which perform respectively "better" with these reads? I'm not very interested in performance, but rather "better" in terms of dealing with the presence of many deletions/insertions.

Options I know of:


BWA  (I think there are special settings whereby I could run bwa
for this case, e.g. see this)
BBMap
Minimap2 attempts to solve a lot of problems that are not properly dealt with by other mapping software. It's written by the same author as BWA, but designed to deal with situations where the reference and query sequences are quite different (e.g. for noisy long reads).