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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.

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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.

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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

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Surely you know that neither bwa nor bowtie by itself is splice-aware?

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  • $\begingroup$ This isn't a limitation of the BWT algorithm, e.g. tophat2 uses bowtie2 $\endgroup$
    – Chris_Rands
    Nov 20, 2019 at 20:54

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