Bowtie2 and Hisat2 which tool should I use?

Question

[ja4123]

Hello! I was wandering what is the difference between Bowtie2 and Hisat2 (not taking into account the algorithm). What tool should I use depending on data I want to align?

Thanks in advanced for reply.

Answer 1

[Carlo Yague]

Hisat2 is more recent, a bit more efficient, and have more features including soft-clipping and spliced read alignments. With eukaryotic RNA-seq data, Hisat2 is vastly superior to bowtie2 because it will be able to deal with introns. With DNA-seq data (or RNA-seq in a species with no intron), you can use either of them, although some might prefer Hisat2 because it is more recent.

[ja4123]

thank you very much for clear explanation