SoftGenetics NextGENe

[bioinfosm]

Anyone know about their tool? or experience using it and how its results compare to what we have in open source?

http://softgenetics.com/NextGENe.html

A lot of biologists are very appreciative of the MutationSurveyor tool.

[ECO]

Funny that you post this up. One of my collaborators just sent me some assemblies from it, if nothing else the screenshots look quite nice!

I talked to the guy at SoftGenetics booth at CHI and he was doing assemblies quite fast on a laptop. Maybe I will email him and invite him to share some info!

[ScottC]

Yeah, I think it would be worth inviting him/them! I spoke with him too and it seemed quite good. I have the trial, but haven't had a chance to look at it yet. I'd be interested to hear any facts and opinions that people have about this software...

[doxologist]

any updates? seems that people are excited... but there have been few that have used it. We have extensive experience with Mutation Surveyor... hopefully, get to play with NextGene soon.

[bioinfosm]

I think its hard to compare them with likes of CLC and DNAstar and others offering similar services.. any people using these have comments?

[doxologist]

perhaps we should ask people from SoftGenetics to comment on this site...

[SoftGenetics]

NextGene software

Hi if you would like a workshop or demo, just let us know...it is rally a different kind of analysis tool...

[lischka]

we are using this for sequence alignment, so far so good.

[husamia]

It depends what you want to do. For targeted sequencing with deep coverage it surpasses all others that I know of. CLC Bio claims to detect deletions in the 5-7bps. I have not tried DNAstar. I did NextGENe trial and I was able to detect deletions of 22bps in both homozygous and heterozygous states. It claims to detect dels up to 1/3 of length of the read. Again it depends on your application. First impressions are user friendliness and performance.

[ntremblay]

Hi, I've used this tool to analyse whole exome data generated on Illumina GaIIx.

The tool is user friendly, the various parameters are all customizable and the interface, although tedious by time (long loading time, counter intuitive mouse usage,etc), is well tough and display all the required information.

It comes with various analysis step (condensation, etc) to explore different side of your data set like snp discovery, small indel, etc. It generates alignment quite easily on a desktop work station with moderate ram and processors.

Some downside too: it's impossible to import your reference genome, snp dataset, etc. There's no way to export data for downstream analysis into other programs. You need to buy a viewer to look at your data out of the main program. and some algorithm (paired-end assembly, etc.) just don't work.

So, it's a nice program that will do the job at the end of the day with little input from the user ... so I would give it a try with the trial and see if you like it before buying it.