Does anyone have a cheatsheet to compare Usearch and Bowtie2 performance in different situation?

Question

[m.koohi.m]

I am wondering if anyone has a cheat sheet or paper that compare Usearch and Bowtie2 performance? I really like to know which one is more robust in different situation. For example I want to search short reads against a database of some contigs with length 150-400. Do you have any suggestion which one of these tools are better?

Answer 1

[h.mon]

I am not aware of a comparison between USEARCH and Bowtie2. If the reads match closely the reference, Bowtie2 would be my choice - for example, mapping the reads used to assemble a draft genome or transcriptome. USEARCH would probably outperform Bowtie2 if reads and reference are not close.