short read aligners 25-50bp BWA vs BWA-MEM vs Bowtie vs Bowtie2

Question

[Agamemnon]

Hello,

If your dataset mainly consists of short reads e.g. 25-50bp sequences, which aligner is preferred? I am specifically not interested 50bp+ alignment.

According to this article: https://www.frontiersin.org/articles/10.3389/fpls.2021.657240/full

BWA is superior to Bowtie2 in end to end matching.

Any specific thoughts or considerations?

[colindaven]

• Use bwa not bwa mem.
• Not sure about Bowtie vs bowtie2, but keep in mind bowtie1 might be very fast, but does not allow indels (typically uses a very long alignment seed).
• Bowtie1 is likely most useful for miRNA alignment.