Hi

What are the best long reads aligners?
I have dna sequencing data generated by minion. Which aligners should I use, I need to detect SNPs and indels downstream

Thanks

[Minimap2][1] is the currently recommended aligner for long read DNA and cDNA/RNA sequencing. If you are specifically interested in large structural variation you should also try [ngmlr][2].


  [1]: https://github.com/lh3/minimap2
  [2]: https://github.com/philres/ngmlr