HISAT (Transcript Alignment) and StringTie (Transcript Assembly)

Question

[komal.rathi]

I just came across this blog. Looks very promising. Was just wondering has anyone tried HISAT and StringTie yet? How does HISAT perform compared to other aligning methods (Bowtie2, STAR, GSNAP particularly). And how does StringTie compare to Cufflinks? Did not find any published papers on these, probably they will be out soon. HISAT was released in July 2014 and StringTie in April 2014. It is surprising no one has used (or even heard?) about these tools. There is no mention of these tools anywhere on any forums.

I am going to try and test these myself, just wanted to know if anyone else is at it too.

[GouthamAtla]

StringTie paper is out. I am going to use it on a simulated dataset and compare results with that of cuffdiff. Meanwhile I would like to hear if you have any updates on this.

Answer 1

[george.ry]

I've been using HISAT (HISAT2 now) virtually since it came out. I previously used STAR, and in my hands the two produce very similar results. Given that, the fact that HISAT2 uses a fraction of the memory makes the switch a no-brainer for me - I can do >2x more alignments in parallel (depending on the size of the datasets).

Answer 2

[Peng Huang]

I am using Tophat2 + StringTie, compared with Cufflinks, StringTie seems to find more genes and transcripts expressed. That's all I could know till now.