Nextgene As An Alignment And Variant Calling Pipeline

Question

[Biomed]

Has anyone used NextGene/SoftGenetics and hopefully compared it with some other popular open source pipeline like BWA+ Picard + SAMtools/GATK? Are there any obvious pitfalls or advantages to using NextGene software or is it simply a preference between paying for an integrated GUI based system vs using a free suite of command line tools?

[Pasta]

I think only biologists care about GUI and would pay for it :)

[Biomed]

I agree but is that the only factor to consider. Are there any issues with data quality, sensitivity, specificity?

Answer 1

[User 59]

In the middle of something along these lines, but only with a focus on 454 data. The company I work with has been using NextGene for some time, and when we surveyed the market for a suitable package for their work (variant detection in amplicon sequencing) it stacked up very well. They're very happy with the output and have no problems validating their variants. I can't comment on it for other applications or sequencing technologies, and have only driven it in 'test mode' a few times.

[Biomed]

I don't have any experience with 454 but I am trying to vet NextGene for Illumina and Solid data. It seems to be very easy to use and there is good support from the company but I really didn't compare it with the opensource pipeline I mentined above.

[User 59]

If we get any comparison results from our study I will post them, but I'm in the middle of moving and having to hand the project over. However I can confirm the NextGene support is very responsive and have been very good at developing features we've highlighted as a priority

Answer 2

[John F]

Why not give it a try, and significantly reduce your bioinformatic support cost

[Istvan Albert]

please expand on this - right now it contains a generic statement that is not particularly useful

Answer 3

[Leszek]

I think we, Bioinformatics people, are very lucky as the best programs for most of our task are free. It's quite unusual situation. My friend worked in Chemoinformatics and there situation is completely opposite. All standard, widely-used tools are commercial, and even academic users have to pay!

Answering your question, yes I think the best currently available solutions are those free solutions you mentioned. Free software usually is widely tested. The code is open and often published, so you know in details how it works. On the other, commercial tools often have got nice GUI and very good support. It's very important especially for inexperienced users. But, free solutions usually evolve faster (anyone can participate) and are highly configurable (or you even can rewrite some parts;) ). In addition, it's free software that is mostly cited in NGS-related publications.

Have a look at this thread as it's similar question.