text: user6530: Burrows wheeler transformation based aligner like BWA or bowtie seems a standard alignment tool used many area. I was just wondering if there is a kind of alignment task in which BWT algorithm is not suitable.
  
  user6273: Not sure about the algorithm itself but Heng Li wrote an article about the future of BWA when releasing minimap2. It gives helpful insights about the topic : Heng Li's blog
  
  user37: BWT based algorithm is just a component of a full-pledge aligner. To that end, it is applicable to most alignment tasks. However, for long-read alignment and metagenomes, we don't often use BWT based algorithms as other methods are faster.
  
original_text: 6530: <p>Burrows wheeler transformation based aligner like BWA or bowtie seems a standard alignment tool used many area. I was just wondering if there is a kind of alignment task in which BWT algorithm is not suitable.</p>
   6273: <p>Not sure about the algorithm itself but Heng Li wrote an article about the future of BWA when releasing minimap2. It gives helpful insights about the topic : <a href="https://lh3.github.io/2018/04/02/minimap2-and-the-future-of-bwa" rel="nofollow noreferrer">Heng Li's blog</a></p>
   37: <p>BWT based algorithm is just a component of a full-pledge aligner. To that end, it is applicable to most alignment tasks. However, for long-read alignment and metagenomes, we don't often use BWT based algorithms as other methods are faster.</p>
  