<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>

CC BY-SA 4.0
2019-11-20T18:43:37.180Z
2019-11-20T18:43:37.180Z
user172818
<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>

CC BY-SA 4.0
2019-11-21T18:25:16.990Z
2019-11-21T18:25:16.990Z
Paul Endymion
<p>Surely you know that neither bwa nor bowtie by itself is splice-aware?</p>

CC BY-SA 4.0
2019-11-20T20:54:05.723Z
This isn't a limitation of the BWT algorithm, e.g. tophat2 uses bowtie2
Chris_Rands
CC BY-SA 4.0
2019-11-20T20:34:17.043Z
2019-11-20T20:34:17.043Z
swbarnes2
<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>

<phylogenetics><bwa><bowtie2>
Is BWT based aligner suitable for any types of alignment task?
# Is BWT based aligner suitable for any types of alignment task?

(Asked by: username_0 on 2019-11-20)

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.

**Tags:** phylogenetics, bwa, bowtie2

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## 3 answers

### Answer by username_1 on 2019-11-20. Score: 3

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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### Answer by username_2 on 2019-11-21. Score: 1

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](https://lh3.github.io/2018/04/02/minimap2-and-the-future-of-bwa)


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### Answer by username_3 on 2019-11-20. Score: 0

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

> **Comments:**
> **username_4**: This isn't a limitation of the BWT algorithm, e.g. tophat2 uses bowtie2  

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