Is BWT based aligner suitable for any types of alignment task? 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.
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.