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

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?

alignment read short
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updated by colindaven 844 • | written by Jalil Sharif 8
  • 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.
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written by colindaven 844

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