text: user1770: 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 
  
  
  user73: 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).
  
original_text: 1770: <p>I have a set of experiments which should result in WGS reads with a high density of indels. </p>
  
  <p>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.</p>
  
  <p>Options I know of:</p>
  
  <ul>
  <li><p><a href="https://github.com/lh3/bwa" rel="nofollow noreferrer">BWA</a>  (I think there are special settings whereby I could run bwa
  for this case, e.g. see <a href="http://blog.liheng.org/2014/12/10/bwa-mem-for-long-error-prone-reads" rel="nofollow noreferrer">this</a>)</p></li>
  <li><p><a href="https://github.com/BioInfoTools/BBMap" rel="nofollow noreferrer">BBMap</a> </p></li>
  </ul>
   73: <p><a href="https://github.com/lh3/minimap2" rel="nofollow noreferrer">Minimap2</a> 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).</p>
  