HISAT2 or SALMON AND KALLISTO

Question

[biks.kestro]

What is good for RNASeq analysis, HISAT2 or Salmon and kallisto ? Please advise if other good option is available.

[N15]

In my sub-field (environmental eukaryotes), Salmon is more popular than the other two, but as others have mentioned below all three are established and respected methods. Salmon and kallisto are extremely similar. I do not have experience with HISAT2.

Answer 1

[GenoMax]

Have you looked at the respective publications/web pages to understand the differences? Since we don't know what your intended application is the answer would be "depends on your needs".

[ATpoint]

Adding on this, all methods are accepted and well-tested. Each has their individual strengths and weaknesses. Please read benchmarking papers for details.