I would say the match has now four competitors:

Tophat2:

• Pros: the classic, the first universally used, still widely adopted in pipelines all over the World, basically people keep using it so their new results are comparable to the old ones
• Cons: slow (several CPU hours per alignment on a human genome with 10M reads), limited to 4Gbases genomes (so, no complex metatranscriptomics for him) and on their very website they say to use HISAT2

STAR:

• Pros: super, wicked fast, the standard used by ENCODE and the big RNASeq projects
• Cons: uses a LOT of RAM, like really a lot (64GB for a human index)

HISAT2:

• Pros: fast and low RAM requirements. If you start from scratch, this is the aligner to pick
• Cons: it’s still new and so many people don’t trust it yet

Salmon/Kallisto:

These are actually not strictly aligners, but rather transcript counters. I put them together for simplicity, but they are different softwares

• Pros: high speed and low RAM requirements. Ideal for quick RNA-Seq gene expression measurements
• Cons: they cannot do de novo transcript detection, sad. They don’t produce counts, which are the expected input for many downstream analysis tools. However, some tools are starting to accept Salmon/Kallisto outputs (in R you can use the transcript abundance import package tximport)

So… USE HISAT! 😀