Which Aligner Would You Recommend For Transcriptome Assembly

Question

[Nicolas Rosewick]

Hi,

An open question : Now there are a lot of aligner available : Tophat, STAR, GSNAP, RUM, .... So which one did you use before performing a transcriptome assembly (cufflinks, scripture,...) ?

N.

Answer 1

[Josh Herr]

This is a topic that is discussed very frequently here. People prefer different aligners based on their experiments and ease of use. There is recent review which has been cited a lot regarding mapping short reads (Tools for mapping high-throughput sequencing data). I enjoyed Mick Watson's commentary on this review too.

I would recommend these review papers too: Next-generation transcriptome assembly; De novo assembly and analysis of RNA-seq data; and Computational methods for transcriptome annotation and quantification using RNA-seq.

Answer 2

[mikhail.shugay]

If it would be a de-novo transcriptome assembly, I recommend Trinity. Trinity could be run in a genome-guided mode, in this case GSNAP is used as a base aligner.

In other case, try Tophat, which I believe is the most commonly used tool, or RNASTAR which is a really fast aligner.