[simonandrews]

It's unlikely that the underlying aligner would have run at different speeds on different systems since they're both going to be calling out to the same code. It seems more likely that the aligners were run with different parameters (different levels of multi-threading, different alignment stringencies etc) which can have a big effect on how long they take to process their data.

[rfilbert]

No, I ran them with the exact same parameters.

[cement_head]

I think that CLC GW is pretty good - we've had it hear for over a year.

[prathima]

Strand NGS, the integrated analysis platform

Strand NGS (Formerly Avadis NGS) is an integrated platform that provides analysis, management and visualization tools for next-generation sequencing data. It supports extensive workflows for alignment, RNA-Seq, small RNA-Seq, DNA-Seq, Methyl-Seq, MeDIP-Seq, and ChIP-Seq experiments.
Pipeline manager option can be used to streamline large scale analysis.

More details on various enhancements/features can be found at http://www.strand-ngs.com/features

[Strandlife]

Strand NGS has improved a lot. The user interface is similar to that of Agilent Technologies GeneSpring, since it is built on same platform Avadis. Strand NGS is very flexible, since its interface auto-adopts to experiment type, only showing relevant analysis steps and functions (i.e guided workflows). You can also customize via R scripts and Jython scripts. Annotation Manager provides access to annotations from within the tool and many more