Spliced aligners for RNA-seq

Question

[amirmhzadeh]

Hello,

I'm working on RNA-Seq data. I am planing to evlaute the performance of the below-listed RNA-seq spliced aligners to find the most befitting one for my study. It is worth mentioning that the species of my interest is homo sapiens.

Right now I am considering the following aligners:

1. TopHat
2. MapSplice
3. SpliceMap
4. STAR
5. RUM
6. GSNAP
7. HMMSplicer
8. SOAP-splice
9. CRAC
10. QPALMA

I know this question has been asked repeatedly over the past few years and there are many great and thorough answers for it but I am wondering if there are some RNA-seq splice aligners out there that I have never heard of?

Any advise would be greatly apprecited.

Cheers,

-A

P.S. I am including some relevant posts from BioStar and SeqAnswers here for future references by the readers:

• How Are Rna-Seq Transcripts Assigned?
• Which Program Should I Test To Map Rnaseq Data? Did Anybody Tried Gsnap?
• Isoform expression quanification from rna seq: flood of tools
• Favorite Splice Site Prediction/Evaluation Tools
• Differentiated expression analysis on isoforms/transcripts level
• Alternative splicing in RNA-Seq
• Novel isoform identification from RNA-seq
• Visualisation Of Alternative Splicing Events Using Rna-Seq Data
• Is There Any Other Method For Isoform-Level Differential Expression Analysis Except Cufflinks/Cuffdiff?
• Best Approach To Predict Novel And Alternative Splicing Events From Rna-Seq Data
• Tools For Visualizing Rna-Seq Splicing Graphs From De Novo Assembly Without A Reference Genome?
• A: Which Program Should I Test To Map Rnaseq Data? Did Anybody Tried Gsnap?
• Has Anyone Tried Rum For Aligning/Counting Illumina Rna-Seq Data?
• Is Tophat The Only Mapper To Consider For Rna-Seq Data?
• Has Anyone Tried Rum For Aligning/Counting Illumina Rna-Seq Data?

[poisonAlien]

HSAT aligner from tophat group.

[Brian Bushnell]

BBMap

Here's a nice poster of it:

http://1ofdmq2n8tc36m6i46scovo2e.wpengine.netdna-cdn.com/wp-content/uploads/2013/11/BB_User-Meeting-2014-poster-FINAL.pdf

The defaults are fine for organisms with short introns<16kbp. For vertebrates or other organisms with very long introns be sure to set "maxindel=200000".

[Lynxoid]

Subjunc -- as fast as STAR.

[khikho]

Segemehl

Answer 1

[h.mon]

Unless you want to write a paper comparing spliced aligners, I would read the literature relevant for your area and pick two or three aligners for testing. Are you willing to optimize parameters for each program, or just use defaults? A program performing badly may just need some tuning.

All in all, it seems just an enormous amount of work, to probably get a small improvement (I am speaking from experience).