Is BWT algorithm suitable for all types of alignment task?

Question

[wuqingkuangsha]

Some widely used aligner like bwa-mem or bowtie2 use BWT algorithm. I was wondering what this algorithm is suitable for, what is the limitation, what is the alternative tool for a particular task.

Answer 1

[mark.ziemann]

BWT based aligners have been applied to most problems already, namely BWA for DNA, Olego for RNA and Biscuit for bisulfite sequencing. STAR is an RNA aligner that uses a large suffix array. There are other tools like kallisto that compare kmer content to perform mapping.